I can't find an edit button anywhere so posting a new post I suppose...

I just wanted to say that the first "bug" i posted in my list above I forgot to cut out. Its not supposed to be there as inquisitors do respawn ;)

Also, I (Milan) had an alliance with the AI (Hungary). Instead of attacking him (he's excommed) and breaking the alliance by betrayal, I did it nicely by sending a diplomat over to cancel the alliance. Doing that got my reputation down from "mixed" to "very untrustworthy" which would have been the case if I had just attacked anyway. Thats kind of silly though as that would mean cancelling an alliance via diplomat is pointless.

Lastly, completing missions etc does not raise your reputation above mixed. But I've seen some AI getting a "reasonable" reputation. But that was an isolated AI that didn't have contact with anyone (Russia)