Thanks guys, I found the source of my CTDs: one of the ESPs was unchecked (because MO sometimes automatically puts ESPs higher on the list when installing mods and I didn't see it)
I also noticed that if you make a change to the ESP list and then click a different tab (like BSAs), when you go back to ESPs the save bar will be grayed out.
@SSL: I think you're right, gotta uncheck everything before choosing Remove Mod