It can be a great campaign, but you need to have enough grasp of it to know what the weaknesses are and how you can compensate.
One of these weaknesses is indeed what Nyarlathotep's role in it is. This is a being who could crush the PCs -- but won't. Why? Or won't unless the GM decides to have this happen. Okay, but most of us would like some guidelines for when it's legit to do this. And it's a being who couldn't get out of a pyramid for millennia, but COULD transport his priestess halfway around the world and insert the entire knowledge of Western civilization into her mind and pick exactly the right idiots to break the trap.
The best solution here is usually some combination of "when the stars are right" (for why N chose to break out then) and focusing on the human cultists. Use Nyarlathotep sparingly, and focus on the individual cultists. Why are they cultists? What do they want? What do they think they're going to get from their actions?
(From that point of view, well, I figure Nyarlathotep is using the PCs to clear away the chaff among the cultists. The big plan isn't necessarily Nyarlathotep's -- if it gets foiled, there's always next conjunction. But at this point, I'm getting off topic.)
For the human cultists, what spells do they need and why? Do they have them in books, on scrolls, or merely in their memory? Forget what the book says they have. What spells do their stats say they know? Get rid of any that don't make sense. Add any you think they really should have. These are what will be in any books they have.
Are these books holy writings of the cult? This seems most plausible in many cases. Does one NPC have a single, closely guarded more general Tome? Go with that.
This also applies to items. The British cult has some items that the PCs could, theoretically, get their hands on. If you don't want them using these items, don't have a user's guide to them. Otherwise, a diary or a sheet of paper folded into the box with the items will do the trick.