Okay here goes:
I encountered a bug in the Telos Academy where there was only the one handmaiden and you couldn't leave with the Ebon Hawk, but luckily I had a save from before entering the academy itself. I read online that it was likely because I had another mod messing with the appearance.2da file that TSLRCM uses, so I deleted said mod. I then realized that I didn't have the original appearance.2da that I needed for TSLRCM 1.8.3, and that I would need to re-install it.
I downloaded the newest version - 1.8.5 - but like an idiot, I forgot I needed to delete 1.8.3 first (really new to this). By the time that I had downloaded 1.8.5, the executable uninstall feature had been changed and I manually tried deleting 1.8.3 by cross-checking all of the files that were still sitting around against 1.8.5. I moved all the necessary data and exe files to a new folder where I had just the RCM to try and isolate the problems, but when I ran the game again it had switched my player character to Kreia in addition to the regular NPC Kreia because I had been using a mod that added the 5th playable head from KotOR 1 as an option. I then reinstalled what other mods I could that had the TSL patcher to work with, like the complete Jedi council mod, the Coruscant expansion, the Hak Pad (still haven't tried that one in-game) and left it at that with the override folder full of all kinds of gunk that I believe, but cannot confirm is RCM 1.8.5 + TSL patcher works mentioned before. The lips bug occurred with all conversations within the Telos Academy (Atris, Handmaidens, Party Members...) and then all of the scenes taking place on the Ebon Hawk directly after you leave the academy. I used the KSE to alter my file to allow me to be a male humanoid pc again instead of Kreia, but I could not find my original body among the options to allow me to equip gear and change the look, but those were the only changes I made with the editor.
To summarize, I screwed up royally.