few question?

1. what causes the relationships with the pope to go down (besides attacking catholic factions).
from my observation: Executing Catholic prisoners (even when the ransom is refused), Sacking a catholic settlement, attacking a catholic army (even if it's besieging your settlement). can some one back this up.

2. How to win favor with the pope? Building churches doesn't seem to do it.

3. What stops factions from being excommunicated? I've been attacked by Denmark, Poland, Venice, France, Milan, multiple times a turn for the last 20 turns, no one has been excommunicated.

4. Guilds. Is it possible to have multiple guilds in one settlement.

1. What you say is true IF you have worse relations with the Pope than your enemy (I don't know about the prisoners). Which gets me to no 2:

2. I give him money and it's working. 1000 florins every time I want the relations to go up 1 point. I think that building churches, recruiting priests and sending them preaching in non catholic regions has to help but I cannot find the pattern.

3. Related to no 1. If the Pope likes you, they will be excommunicated first.

4. No, not in my games.

I believe that if youre excommunicated then other catholic factions wont face any negative consequences for attacking you. Same thing if you attack an excommunicated faction.

1. Like Nestor says, whatever factors that make your pope-o-meter drop also take the existing value into account. Attacking a christian town will only make the pope really hate you if 1) You are a stronger faction than the faction you're attacking (I think this much matters more than who attacked first, may be wrong though) 2) You've been pissing him off/ignoring him consistently 3) They are more in favor than you are. Of course, anytime you do things that angers the Pope your relations with him will worsen, but by far and how he reacts (from calling for peace to sending inquisitors to excommunication to calling a crusade against you) depends as much on the relative favor of the belligerents as it does on your own absolute favor. A 10 favor Venice burning a 0 favor Paris to the ground will result in polite silence.

2. Building not only churches, but the best kind of church you can fit in your cities pleases him.
Preaching up christian % either in your own lands or abroad pleases him.
I think freeing christian prisonners without asking for ransom also does. Fielding as many priests as you can muster obviously helps, if only through the heathens they'll convert each turn.
Crusading is a given, and you don't even have to succeed either, you'll get points for trying even should your army not leave the coast of Ireland, so long as you had it join a declared crusade (or course, if you join but don't actually go, your army will die out quickly to desertion).
Sentencing heretics and witches also seems to make him happy.
Having voted for him makes him your best buddy too, with bonus points if he was one of you own cardinals before donning the funny hat.

Other than that, regular diplomacy with the Papal States faction also works - giving him money/land/maps, a long lasting alliance and trade rights, sending armies to help his when he's going macho on brigands in the Roman countryside... Whatever keeps regular AI factions happy keeps him happy too.

3. Could be that you're the stronger faction, so in a David vs. Goliath way they're seen as plucky underdogs while you're the bully, even though they really are the ones doing the oppressing. Could be that relative pope-o-meter thing. Could be the Pope's origin too. Also, I think the pope's violence and purity ratings have an effect - a violent pope will perhaps turn a blinder eye to low-scale warfare, and a pure one will perhaps care less for favor and look into actual actions more. Wishful thinking here.

4. Nope. One guild type per city, although it can eventually be upgraded into a better version of itself when the city grows big enough to house it and whatever caused it to be offered to you in the first place still happens.

2. Churches not so much but the pope loves cathedrals. Make one of those and you'll get a message saying how he likes you more. I made lots of them and my relations with him is at "perfect", I got 10 crosses, and he doesn't even care that I am smashing Denmark who are not excommunicated.

2. Vote on the winner.. If you vote wrong, it's a bad start.. Crusading has been mentioned, but musn't be underestimated. I was constantly warned by the pope for attacking others, while only one was started by me (poor little poland). After I won a crusade, I feel like I'm the favoured son.