Bec

I also encountered your issues 2 and 3. For the "companion as pet" issue, I was playing as a Ranger(/Rogue) with a bear. I ended up with a second bear after I died and reloaded the area, and the second bear proceeded to follow my party and fight alongside everyone in my party whenever I went anywhere else (it would wander over towards the party as soon as I entered a new area). My bear's name also changed from "Theodore" to "Bear Companion" after the second bear appeared, and my ranger had "Bonded Grief" stuck on them permanently. After quitting the game and starting it up again "Bonded Grief" went away, but the second bear remained and my bear is still "Bear Companion" instead of his name. For the "Quest Completed" issue, I had the exact same problem with the exact same quest upon completion. I also noticed that the journal entry for the quest after completion was a bit wonky: Here are my saves and my output file, if needed!