What Could Have Been: John and Dave and the Temple of X'al'naa'thuthuthu, the prototype of the book. Still featured spiders, Falconer, an infected zombie cop named Frank, and them, with several large differences.
The zombies don't mutate. Much. They are, however, bulletproof, super-human, scream in a thousand languages unknown to man (and scream loud enough to knock anyone in a mile radius out), and, if killed, are retrieved to birth more spiders.
"Them" are vaguely beneficial - one shows Dave the location of Franky's corpse, which is set to hatch a thousand spiders in the school and tells the trio that human will is the only thing that can stop the outbreak. They, however, do drive Detective Falconer to suicide, albeit only because he was infected and dosed with Soy Sauce.
The Shadow Men have a much larger role by being the ones behind the outbreak and possessing several people. Also, here, it's outright stated the Shadow Men took Amy's hand in the first place.
The site of the mall from the first book turns out to house a gigantic stone tower that's only visible to soy sauce users.
The spiders break out and infect an entire elementary, which would have lead to John using this line:
Remember, these are children. Aim low.
However, Amy really isn't keen on shooting up a bunch of kids. Dave is able to use a fleeing Shadow Man's portal to jump back in time to himself twenty minutes prior to stop it by summoning a giant meteor to destroy the school after they manage to evacuate it.
Falconer commits suicide after learning he's infected.