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?

i don't know if this will help you but i tried talking to Nauxus first since you cant talk to Axel, after talking to nauxus when you come back to the tavern, witer will tell you that thane has woken up and asked witer to give  the bloody cloth to you, which you will use to the paintings stuff, don't worry you will not continue siding with Nauxus, unless you gave him the toadstools for poison. if you also encounter the problem where you can't start the "hell's kitchen" side quest, try talking to meko first

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.