To keep things simple, helped Thane for the first 2 parts, tried giving the fruits to both sides, the guide says to talk to Thane in the tavern after (I'm fairly sure?) After he gets injured, but he doesn't stay at the tavern for me, he ends up taken back to the bull village by the healers.

I'm trying to figure out if I did something wrong, or if he somehow ends up back at the tavern later, but trying to go through part 4 put me on from what I could tell to be Nauxus' route. When am I supposed to be able to get the bloody cloth from him, so I can use the emblems to go through the paintings? Or am I just misunderstanding the whole thing?

Just remember you have to save the shark before all of this. I think or say good bye for Thane in the worse way possible.. I .. cried when that happened with me.

For me, Thane didn't come to the tavern until after I had brought peace to both sides.  Before that, I was on the Thane/Nauxus route and had been asked to deliver the poison toadstools.  I did not deliver the toadstools since that would have triggered the ending where Thane and Axel die.  Instead I wandered around until I was delivered Thane's bloodied cloth.  I don't remember if I received it while in the tavern or the bull's camp.  After I received it, I was able to enter the pictures, find the shapeshifter, and end up with the 'good' route where both Thane and Nauxus were at the tavern.