|Power. Tyranny. Destruction.|
The best suggestion I can give you is to ditch the caravan rules. They are at best a headache (as you're discovering) and at worst aren't balanced against some of the encounters as written (see plenty of other threads on the subject).
I started incorporating a pared-down version of the caravan rules into my game that removed the extra tier of non-character-level rules i.e. the caravan stats. However, I've recently found that even these rules are becoming a headache to incorporate and keep the verisimilitude of the game. This AP puts plenty of pressure on a GM with the tag-along NPCs as it is, you don't need a bunch of rules on top of that, especially rules that don't quite work right.
I have begun thinking of ways that the party can ditch the caravan altogether and it will make sense for the story and the PCs and the NPCs. I'm very much looking forward to that day and bringing this campaign back to focussing on the PCs and not having them feel like they're being led around by the nose by events and NPCs and aren't in control of their own destinies.
Basically, what I'm saying is, if I could start this AP again knowing what I know now, I wouldn't have had the caravan involved at all. Heck, if I couldn't convince my players to take the roles of the NPCs I'd probably have left most of the NPCs out of it too so that the players can realistically take the spotlight and aren't wondering why they're doing all the legwork.