In Oblivion, when you wanted to start a quest mod over or "reset" a mod you would deselect it in the launcher, go back into the game and save without the mod installed, and then select the mod in the launcher again and play as you normally would. Things seem to work differently with Morrowind mods, I'm finding that companion mods (Specifically "Gatanas") and even the official expansions will retain all data in your save game files, whether the mod is installed or not. I can't start the quest with Gatanas again, the DB assassins who attack me are completely naked because I've looted their corpses from when the expansion was installed, journal entries are still intact from long abandoned mods, etc..
Is there any way to clean a save file of this information? I've tried loading up a save file in the CS and its an absolute nightmare. There must be at least 300 different entries to sort through.