Safehold/WMG

Langhorne and Bédard have PICAs hidden away underneath the Zion Temple

Those are the power sources that Merlin detected long ago and that have worried him ever since.

Langhorne and Bédard, not wanting a silly mortal thing like death to take away their divine status, downloaded their personalities into PICAs like Nimue and placed them into hibernation underneath the temple in Zion.

They didn't awaken after the real folks' deaths because of their egos: The PICAs are kept in hibernation until a major crisis, such as the current schism with Charis, requires their awakening (see the WMG below this one). So, Langhorne and Bedard awaken, smite the heretics like Big Damn Heroes, and permanently cement their divine status among the residents of Safehold. Emphasis on permanent, since PICAs are effectively immortal.

But Zion and the Temple were built after Commodore Pei blew Langhorne and Bédard into radioactive dust. If the surviving members of the Operation Ark command team had PICA backups for Langhorne and Bédard, why didn't they activate them right away?
The temple was built on the same location as Operation Ark's original base. PICAs belonging to members of Ark could easily be there. They weren't activated right away because the surviving "Archangels" didn't know about them.
- Another reason they wouldn't be activated right away: Langhorne and his followers couldn't break the PICA 10-day activation limit like Nimue's group could. If Langhorne did ever return, then it would be only for ten days, making it useful for only the direst of emergencies.
  - The problem with the idea they couldn't break the activation limit is that Nimue's group did it in a few weeks, while Langhorne and Bedard's group would have had nearly a century to break the lock (10 years in hyper + 20-30 while Shan-wei terraformed + 60 from creation until they died). Langhorn was insane, not stupid. Hell, as the colony leaders they probably could have gotten the Terran government to make a special exemption and gotten themselves 1 or 2 PICAs without the limit under the justification of having permanent advisers for the colony. They didn't have any problems about lying to the government about their intentions in other things after all.
Word of Weber, or at least word of Barnes & Noble is that Merlin will learn what's underneath the temple in How Firm A Foundation.
- And this is highly implied, if not stated outright to be the case in book 5, with a strong possibility that said PICAs will be activated in roughly twenty years.
  - Book Five also addresses the above issue about whether or not Langhorne and the rest could have broken the ten day limit, as it seems that the one who did it for Merlin himself was particularly knowledgeable in that field. There's no concrete certainty on it, but alternate ways around the limit are suggested.

About the Key.

The Key awakens the Langhorne and Bédard PICAs: Samyl Wylsynn revealed in By Heresies Distressed that his son Paityr has a "key" that could be used to do something big. Since we saw Paityr and his "truthstone" in Off Armageddon Reef, it's not hard to believe that he has some more Lost Technology of his own. That "key" is the means to revive the above-mentioned PICAs of Langhorne and Bédard. On the other hand...
- The Key activates the Rakurai: If ever the Church had a weapon of last resort, then that is it.
- Rhobair Duchairn now has the "Key" as well. It has to be part of what Hauwerd Wylsynn passed Duchairn.
  - According to Paityr Wylsynn in How Firm A Foundation, and elaborated on by Merlin, the Key is a device easily mistaken for, and used as, a paperweight which, when combined with the Stone of Schueler he has already, provides "Visions" (Holograms), among which is a message from Schueler himself. The message provides information on the chamber under the temple, among other revelations. It also can be used inside the Temple to activate a weapon that is only to be used against a great threat to the Church, as it can only be fired once. This is quite possibly the Rakurai, though whether the one shot limit is due to the weapon, the Key, or just something Schueler said to make sure his descendents didn't fire it wastefully is not said.

In the Grand Finale, OWL will use the Rakurai will be used to finish off the the Gbaba

It is a nigh-indestructible weapons platform that can be activated at will by anyone with the right passwords and that can probably be turned toward something outside the planet.

Also, it would be awesome.
It would also make no sense. The Gbaba destroyed the entire Terran Federation, including Earth. That's the premise. They are too big a menace to be threatened by a single planet's worth of orbital weapons. They'll just launch a volley of WMDs at the planet on a ballistic course from beyond the range of the Rakurai platforms.
Rakurai is only nigh-invincible because Merlin and Owl don't have enough Dakka to get through it's defenses and no way to get more currently. Additionally, it's basically just a giant asteroid launcher, most of it's power comes from Safehold's gravity. If the Gbaba get close enough for it to be used as a weapon against them, humanity is screwed.
Correction, then: It will fire off the final shot.

Siddarmark has an equivalent to the Brotherhood of St. Zherneau

Republic style government, leaders work for better human rights and to listen to the people, and it's been implied the only reason it's not on Charis's side is their populace wouldn't support them. It's founders could have easily modeled it on the Terran Federation. Siddarmark built up its pikemen (largest army on the planet remember) for the same reason Charis built up it's navy, protection from the temple in the inevitable conflict.

Zherneau mentioned in his letter that there were others like him, but he didn't know where they were sent or if they even survived Langhorne's attack.
Also take into account Clyntahn's automatic suspicion of all things Siddarmarkian. Whatever else he may be, Clyntahn's instincts have thus far led him to be Properly Paranoid where this sort of thing is concerned.

Merlin will make use of the Rakurai.

It is activated by large energy signatures. It might be as simple as creating an electro-magnetic pulse near the desired target.

The fleet sent on Operation Breakaway survived.

Realistically, there's no way Safehold could advance to the point of being able to defeat the Gbaba - when the Terran Federation couldn't - without outside assistance. Therefore, Weber will introduce a Terran faction that has managed to survive this long, and that has a way to defeat the Gbaba. However, they lack the necessary numbers. That is what Safehold will provide. And who better than the Breakaway fleet?

Though the Federation thought they weren't too far away from technological superiority (so numbers wouldn't be as big a factor) and the Gbaba probably won't have advanced much. Earth started with one planet and didn't have a PICA to kickstart the whole process of development. Given (lots of) time Safehold could do it too. Plus, the entire point of the operation was to convince the Gbaba that they'd destroyed the entire fleet. If the fleet had survived Breakaway, the Gbaba would keep hunting until they found them, possibly finding Safehold in the process.

Schueler had a Heel Face Turn.

Whether it was an My God, What Have I Done? moment when he saw what his Order had become or would potentially turn into, or if he was turned by Shan-wei against Langhorne, or both, Schueler the man turned against Langhorne's grand plan in the end. Potential foreshadowing comes from A Mighty Fortress when Merlin annoyingly wonders, in regards to the Order of Bédard, why the original villains of the piece can't remain so. There's also the fact that the only known piece of pre-Creation technology other than Merlin that's outside of Church control is Paityr Wylsynn's Stone of Schueler. Speaking of the Wylsynns, Hauwerd remembers his brother telling him that there was a legend that said the Wylsynn clan, long-time advocates of reform, was descended from Schueler himself. He could well have been the Duchairn of his group, understanding they were wrong but ultimately powerless to actually stop it.

Not necessarily powerless. The entire Book of Schueler could be a Batman Gambit. The punishments laid out in the book are horrific enough to sicken many people who watch them carried out. Perhaps Schueler realized this and wrote the book that way deliberately. People being people, someone would eventually go overboard carrying those instructions out, and people would be horrified enough to begin questioning the church. And remember that Commodore Pei mentioned that one other knew of his plan. That one other might've been Schueler.
How Firm A Foundation suggests that Schueler may never have written the Book of Schueler at all. It was instead someone else's work attributed to him. The messages Paityr Wylsynn describes paint him as the kind of Archangel the Wylsynns would have every reason to revere.

Earth survived

And there were forty one other secret projects running in parallel to the Safehold project. All forty two of them being released simultaneously during the siege of Earth.

Owl's developing AI is the result of human interaction

In A Mighty Fortress, the artificial intelligence Merlin was promised Owl would develop finally began to stir. This is after three and a half books and about two or three years. The most likely trigger: Bringing more people into the Inner Circle. Owl's AI began to develop because he finally began interacting with actual human beings as opposed to a PICA. The reason this is significant is because we saw, via Paityr Wylsynn's Stone of Schueler, that Old Earth tech could differentiate between a living human and a PICA. What reason is there Owl couldn't do the same and, as a result, never developed the AI that comes with interacting with human operators because, as far as Owl ever realized, he never was interacting with a human operator.
I find it more likely that Owl's developing AI is the result of having more people to talk to. Weber's made a point of having Merlin's humanity confirmed in a spiritual sense; I don't think he'd undermine one of his own themes that way.
- My thinking isn't so much the result of Merlin not being human in the moral sense. But that his lack of humanity in the physical sense is the issue.
- It might be something more along the lines of training. Nimue has years of experience with computers like OWL, and therefore Merlin knows how to phrase commands and instructions to get it to do what he wants. The others who start talking to OWL don't have that training, so the computer will have to learn how to interpret what they're asking it to do, rather than just following Merlin's instructions, which fall into—or close enough to—its' normal input parameters that it doesn't have to develop new ways to deal with them.

The Rakurai will destroy Zion

Someone, be it pro or antagonist, will discover how to launch the Rakurai and use it. The end result will be that the Rakurai hits the Temple Lands and destroys Zion. What better way to truly destroy the Church of God Awaiting than to have its capitol destroyed by what Safeholdians believe to be God's ultimate weapon? It could even help pave the way for the worldwide revelation about the truth of Langhorne.

If this happens, it's far more likely to be the antagonists who trigger it accidentally than the protagonists. It would kill at least hundreds of thousands, probably millions, of civilians so Staynair would vote against it on humanitarian grounds. Merlin, Cayleb and Sharleyan would probably vote no for the same reason. The only person on the protagonist side likely to do it is Peityr Wylsynn, but that would require him to disappear to the temple to use his key, assuming that's what the key even is.
- Even disregarding the humanitarian grounds, Merlin wouldn't allow it because it would make his job of subverting the Church much harder. Rakurai obviously existing would reinforce the religion in virtually everyone who doesn't know the truth. Most of the planet would view it as God came in and annihilated the corrupt priests in Zion who used his name for their own evil ends. GO GOD! GO LANGHORNE!
  - What? Some of the Charisians are claiming Langhorn lied and Shan-wei was good? But Rakurai is REAL and God and Langhorn use it to kill the worst of all sinners! Obviously Langhorn didn't lie and Shan-wei was evil. WE MUST WAR AGAINST THESE NEW HERETICS IN CHARIS!
  - That makes absolutely no sense. Merlin isn't trying to deny the existence of either the Archangels or Rakurai. The documentary evidence for their historical presence is too vast to wave away. On Safehold not believing in their existence would be like someone now not believing the Roman Empire really existed. And even aside from his desire to be truthful, convincing everyone the Rukurai didn't exist at all would have some dire consequences down the road. The only reason not to use the Rakurai on Zion would be because of the number of innocents who would be killed, and because when the truth about the Rakurai came out and they could no longer blame it on God they would have to admit that they'd intentionally murdered all those innocents just to get at the group of four.
    - He isn't in the short term, but that's more a tactical necessity than anything else. His long term goal is to return humanity to a technological society and teach them the truth about history. That will of necessity include teaching them the truth about both the Archangels (they existed but they were humans, not angels) and the Rakurai (it's just dropping rocks at very high speeds). Using the Rakurai before people have the chance to understand at least the basic physics behind it would have exactly the opposite effect, reinforcing belief in divine intervention from the heavens.

Nimue/Merlin will return to a female form on a part time basis in the not to distant future

As of A Mighty Fortress occasional use a PICA's ability to alter its appearance to a limited extent is being used to create the appearance of a network of seijin of whom Merlin is merely the public face. While this is useful primarily to avoid rumours of Merlin being in two places at the same time (or at least moving faster than possible with the normal means of transport available on Safehold) it strikes me as the perfect opportunity to engage in a bit of social engineering and help establish a precedent for greater gender equality in the form of one or more female seijin running around.

Admiral Thirsk will be assassinated by someone under his command for supposed Charisian sympathies

The series is basically the Thirty Years' War IN SPACE!, and Thirsk is pretty similar to Albrecht von Wallenstein.

According to Word of God, a named character will be Killed Off for Real in book 5. Who's most likely to kick the bucket, why are they, and how will it happen?

Since it was said to be a character he liked, and the tone of the tweet was that it wasn't a nice way to die, there's a couple of obvious possiblities.
- Admiral Thirsk, he's unpopular with Clynthn and hated by the man in charge of his navy who's name I can't remember, and other nobles in his kingdom who don't like his growing power. Being brought up on heresy charges because of other nobles bribes to the inquisition is possible.
- Earl Coris, he already heavily suspects the Church was behind Hectors assassination. Finding proof of this then getting killed by church loyalists is likely, though I can't come up with a situation where Irys and Daivyn aren't arrested immediately as well.
- Princess Irys, the biggest trait she's had in the series is she doesn't change her mind on something once she's decided on it. If Coris finds proof of the church's involvement in Hectors death, it's entirely possible she may not believe it, Coris and Daivyn barely escape after she reports him. Without anyone else to make an example of, Clyntahn has her arrested and executed for her families 'heresy'.
- Prince Daivyn, Coris finds evidence, etc. Daivyn is killed, but Irys manages to avoid execution due to being a girl. She escapes back to Charis, blah, blah blah.
- Archbishop Cahnyr, he's loved by his archbishopric, which is a part of Siddarmark. If the inquisition finds him, his death could send Siddarmark into open alliance with Charis.
  - Problem with this is that Cahnyr may well be in the Empire of Charis now. He certainly seems to have been the senior member of the Circle to have survived.
    - He never says he's on his way to Charis, the only end destination he gives is Siddar City. Given Siddar City is a port, he was probably planning initially to go to Charis, but at the end of his chapter he learns about a fairly large support network for him in Glacier heart, set up by Ahnzelyk Phonda. I think he's more likely to stay in Siddarmark and try to turn the country against the temple. From a purely storytelling point of view, he's a completely pointless character if the only thing he does is escape to Charis. There's been several of those, but all of them did more than just go there.
- King Gorjah, Clyntahn already suspects him, and he's probably going to be a major character in Foundation.
- Cayleb, killed in the book's final battle, time skip of 10-20 year between Foundation and book 6. Book 6 focuses on Princess Alahnah and the next step in getting Safehold back in space. Would require Clyntahn to die and Duchairn to become Grand Vicar and recognize the schism to justify such a skip (a fair trade?)
- Duncan Yairley. He's Hektor Aplyn-Ahrmahk's mentor and is a fairly important named character outside the main protagonists. Also, in some of the released snippets from How Firm A Foundation, his ship is apparently going to get into a major storm and possibly crash. Getting captured by the Church could fit right in there, with Hektor stepping up into his place.
- There's plenty of minor characters that could die, like Kynt Clareyk.
  - The implication behind a "named character" being offed is that said character will not be either a red- or mauve shirt. Though someone might wind up joining the main cast only to die.
  - A Mighty Fortress does begin with Kynt Clareyk promoted to second-in-command of the new Imperial Army, with Merlin considering bringing him into the inner circle, so he specifically seems susceptible.
Turns out it's among others, Gray Harbor and Nahrmahn in the attacks by the Rakurai group, and Gwylym Manthyr, in Zion.

Commodore Pei mentions in his last message to Nimue that one other knew of the backup plan (i.e. Nimue's PICA). Who was it? And will it matter at all?

It has to be one of the "Angels" or "Archangels", but so far the only members of that group who have received more than a passing mention—and aren't named Langhorne, Bédard, or Pei—are Schueler and Chihiro. And Chihiro wrote most of the Writ.
- I'm inclined towards thinking that it was one of the unnamed ones. The Commodore's message implies that the one other who knows is coming with him on his suicide mission (he says something like "and we both have an appointment") which would seem to rule out Schueler. While we don't know for sure the fact that Schueler was credited with the Book of Schueler after Shan-Wei's rebellion would suggest both that he survived the war and was loyal to Langhorne (or at least convinced everyone that he was loyal).
As for "will it matter" - the fact that the predicted time of the Archangels' return, so very close to Nimue's own awakening, can't be a coincidence. Who knows, maybe the awakening was planned to assist Nimue's mission!

Clyntahn will violate the Proscriptions first.

While the Inner Circle has done their level best to dance around the proscriptions, even after Father Paityr helps them run Loophole Abuse. Clyntahn's a self-delusional hypocrite. Despite toppling the Proscriptions of Jwo-Jeng being the protagonists' stated goal, there's a legitimate chance Clyntahn will be the one to openly violate them first. All in the name of God and protecting Mother Church from filthy heretics, of course.

- this is supported by the conversation Merlin and Cayleb had after Cayleb got let in on Merlin's secrets, about defeating the Church by forcing them to change their belief structure.

Duchairn will be the next Grand Vicar.

Nobody in the Vicarate likes Clyntahn, especially after what he did to the Circle, but nobody dares openly act against him for fear of the same happening to them. But Duchairn has been passively defying the Grand Inquisitor, openly disapproving of his actions by conspicuously refusing to do anything that might be seen as tacitly approving of them. Between that and his newfound interest in good works, he's slowly gaining public approval. The Inquisition is watching Duchairn to ensure he can't build an open power base to oppose the rest of the Group of Four, but the death of a Grand Vicar can completely rearrange the political playing field. Duchairn could find himself chosen to replace the politically irrelevant Erek by all the Vicars who approve of his opposition to Clyntahn and use the power base of all the people who supported his elevation to stomp Trynair and Clyntahn flat.

A potential Chekhov's Gun to help with this: Duchairn is currently being "protected" by the Temple Guard, whom he assumes are also spying on him for Clyntahn. We know, however, that his head guard is in fact the captain who killed Hauwerd... who happens to be honest and genuinely devoted to his duty and his faith. This has potential...

Merlin's "personal project" with the VR unit involves resurrecting Nahrmahn

The silver mesh device he put over his head on his death bed wasn't just to reduce pain and wake him up so he could say goodbye to Ohlyvya. It was also scanning his brain for use in a VR or PICA. The VR unit Merlin has Owl working on is supposed to be able to support a couple people, so he can use it to boot up a copy of Nahrmahn as well as providing a backup for himself. And if the copy doesn't suffer from Merlin's inability to do high speed downloads of data...

Something's hidden at Armageddon Reef.

One of Cayleb's ships, the Wyvern, goes flat-out missing during the battle of Crag Rock. Poof, gone, not a hint of wreckage or crew to be found... not even by Merlin's satellite reconnaissance. Suggesting that there's something in the area that is invisible to satellites. Perhaps Chihiro and Schueler were right about the military personnel of Operation Ark being less than pleased about Shan-wei's fate, even after Langhorne met the pocket-nuke.

The power signatures under the Temple include some kind of weapon intended to be a last-ditch defense against the Gbaba.

After all, they couldn't be certain the Gbaba would never catch up...

Related: The Holy War is derailed when someone does wake up all those power sources under the Temple... which proceed to catch a Gbaba scout ship's attention. Cue a desperate scramble to take it out before it can report back, where Merlin, who has been playing second fiddle militarily all this time, gets to demonstrate why Nimue was considered a tactical genius in spaceship battles.

Marrying off Irys and Daivyn.

So Irys and Daivyn are safely headed to Charis and it seems likely that they will eventually swear allegiance to Charis (since the Church will no doubt kill them either way, they might as well throw in with Charis). When that happens it seems likely that Cayleb and Sharleyan will arrange political marriages for one or both of them to tie their families together. With that in mind I see a few possibilities:

Irys and Nahrmahn Jr. This is a reasonably logical pairing, they are of similar ages and Nahrmahn Jr. is one of the most important nobles in the Empire.
Irys and Hektor Aplyn-Ahrmahk. This would have the advantage of tying Irys directly to the royal family while also keeping her out of the succession (since she's very ruthless when she decides to be which makes her a potential risk).
- Also, it's entirely possible they'll get to like each other on the trip from Delferahk back to Charis.
Daivyn and Zhanayt Ahrmahk. Again, relatively similar in ages (I think) and it would tie the Prince of Corisande to the Imperial Family. Additionally, this possibility was alluded to in an earlier book where Sharleyan mentioned that it would probably be necessary to marry Cayleb's sister off to whomever they ended up putting in charge of Corisande. Given that Daivyn is probably a better match for her than many of the other candidates (he seems like a nice young man).
Daivyn and Alahnah. A very wide age difference, although not unreasonable compared to some political marriages in history. I think it's unlikely just because of the squick it would cause for modern readers but it is a valid option.
- This is probably less likely than the other possibilities offered here, since Daivyn is the only possibility for Prince of Corisande, while Alahnah is currently the sole possible heir to the imperial crown of Charis.

What stories was Merlin telling Daivyn?

It's not specified in the text, but it's supposed to be fantastical fairy tales that Irys had never heard before.

The Hobbit, perhaps?