I'm sorry that you don't want to remove a mod and i sympathize but a mod doesn't need to have a missing content message to have it cause you to crash to desktop at anytime either at startup or several hours into play, For example i had a load order of 200+ mods and it was stable for months and then i trimmed it down to about 70 and added a few new ones and then i got constant crashes,
Anyway the point is i narrowed down which mod caused my problem removed it, added a few dozen other mods and it was a lot more stable than the 70+ order ever was. The whole point is just because you cleaned your mods, sorted them and have no obvious errors doesn't mean that one or more of your mods isn't screwy