Anyone ever encounter this where a mod continues to run even after you remove the files? How do you get away from this?

Does it involve scripts? Sometimes those can stay in your save file. I think there's usually a specific method of shutting down and uninstalling mods that involve scripts.

Yes there are scripts

It's really hard to remove script variables from savegames unless the mod also had an inbuilt "uninstall" feature that allows the script data to be removed from your savegames. Most mods don't have that so most of the time you'll need to start a new game if you want to have a clean savegame free from old scripts/mods.

How does one create an uninstaller for a mod then?? :/
And sheesh man this is kind of strange ... I never would have expected to have something like this happen. What if I just rename every variable and quest to something new?

http://www.gamesas.com/topic/1386485-uninstalling-scripts-vs-leaving-them-in-but-replacing-with-blanks/page__p__21038069#entry21038069