John Dies at the End/WMG

The spider Robert North gave Monster Dave was Dave's soul.
That's why we don't see a ghost of Dave.

The spider Robert North gave Monster Dave removed Korrok's ability to alter his cells.
When Korrok spoke of things such as being able to, for instance, turn him into a child molester, it was bluffing. This is a good explanation for why Korrok didn't rewrite Dave to bring things back under control as soon as Shit Narnia started to hit the fan.

Molly turned into Fred Durst to drive Dave and John home
Durst even says "...I've been dogging you this whole time."
 * Yeah, I was wondering why Dave didn't catch on at that point. Probably because his more observant half was sitting in the truck bed.

Molly is an angel.
Or something similar.

John DID die at the end... sort of.
He contracted a case of the "bloodworms" or whatever in the other universe they found on the basketball court. The air in the normal timeline is wrong for the things to propagate past him, but they'll still inevitably cause his death.

Alternatively,

John will die at the End.
The End just hasn't come yet.

Korrok is 4chan.
Rather obvious, frankly.

JDATE is one of the multiverses mentioned in Tengen Toppa Gurren Lagann.
John is this universe's version of Kamina. Likewise, Dave is Simon, Amy is Nia, Molly is Boota, and the Shadow Men are Anti-Spirals. Korrok and company are equivalent to the Beastmen, or perhaps Spiral Races who don't give a damn about the Spiral Nemesis and are charging recklessly ahead to exploit the power of life (explicitly called out as the greatest in the universe, not unlike Spiral Power).
 * The Shadow Men and Korrok are explicitly working together, however.

John DOES die at the end...
Because at the very end of their adventures, he time travels back to the beginning of the book and goes into that police interrogation room, and then dies, while the REAL John who belongs to that time survives until he will inevitably go back etc.

John is insane
John has horrible hallucinations, both audio and visual that force him into beliving that he is fighting demons, that are not actually there. In this theory, John and Amy do not exist, they are illusioned people that John has created because his crippling co-dependancy has driven him to create anyone else that might be his best friends. His insanity is slightly managable and does allow him to hold down a job, but whenever he gets bored, or lonely, he begins to invent these odd situations and adventures.
 * Erm, I think half the mentions of John in the above WMG are meant to be Dave.

The title is accurate.
The portal at the very end of the novel was a trap. John stepped in and got knifed by his evil clone, who then took his place.

Molly/Fred Durst is Todd

 * That gives this troper chills. The whole Todd thing bothers this troper on some deep level.

John Does Die At The End...
Of the original story as it existed when it was originally posted online. It ended not long after John dies at the police station. The title was just too damn good to change.