Hello, I just recently found out about this restoration project when I decided to finally finished Kotor 2, there are three main bugs i've run into that I haven't seen before.
The first, and most annoying one, is Bao-Dur having completely broken dialog options, when I first got him on Telos, before having him try to initiate a conversation, just asking what I wanted, it listed "What did you want to talk about?", and I could already ask him what parts of my Lightsaber I had collected, both of these were already there when talking to him on the surface of Telos. Additionally, as I went through his dialog options, they went away, like normal, once I got off Telos, he only had two dialog options, Lightsaber parts and Shields, I got the Lightsaber assembled, and so he only had shields left. He is now at maximum influence, He started a coversation that led to me having the option to ask what he wanted again, but other than that, no dialog options have opened, despite clearing one and a half planets so far, I think this bug has caused him to not be able to ever have a class change.
Secondly and Thirdly, on Dantooine, Despite nearly clearing the planet(i've gotten to the big battle), Akkere still won't offer to sell me Thorium Charges, and Zherron won't give me the mission to give a letter to Dopak.