I was having alot of trouble with inquisitors early on in the game due to my low standing with the Pope, and nothing I was doing seemed to help raise my standing with him. So I just tried to stay under the radar, but inquisitors started flooding France and I found a good way of distracting them. I built a ton of priests. The inquisitors seem to put priority on them, as they were burning my priests every turn, but never got to my generals. Later on, I found out that simply giving the Papal States a ton of money raised my standing with the Pope by miles, and his inquisitors stopped coming after me. So distract the inquisitors with your priests, until you can bribe the pope.

On a side note, how many hours straight have you guys been playing? I hopped onto my computer at around 11, started playing, and next thing I knew it was 5:30! I've never had that sorta time-lapse with a game before. Best Total War yet.