Starbase503

I am curious. I used LOOT and TesEdit to clean up my ITM and deleted references issues in my mods. However, LOOT still lists several of those in the main files (Update, Heathfire, Dawnguard and Dragonborn). Last time I played it crashed to desktop while inside The Bannered Mare, a common problem area for a lot of people. Could this still be a mod affecting this, or do I need to clean up those main files' ITM and deleted reference issues?

my game crashes or freezes just in Whiterun, but do I have to or should I extract EVERY bsa file, or are there specific ones that will help Whiterun's stability? I unpacked the Ladies of Whiterun mod's bsa files, but not sure which others would help.