I just said screw it and started from scratch. I've run into that issue before, and it's almost always because of mismatched textures and models. Since most of the model/texture replacers that I used involved a ton of loose files, I figured it would make more sense to just install one mod at a time and test, painful as that may be. I didn't exactly relish the idea of popping everything open in NifSkope, trying to figure out exactly which mod pack it came from, and trying to figure out which files it actually needed.
I fooled around with Project ENB a little bit. I looked at Realvision, but it looked a bit too surreal for my liking in the screenshots (if you want to turn me off from a graphics mod, liberally include lens flare in your screenshots...I had enough of that in the late 90s, thank you very much). I'm going to give Vividian a shot...the weather effects in it look gorgeous, and it seems like it's a bit more comprehensive than other ENBs, as it includes a mod as well.
I've gotten pretty good at repairing Skyrim when I went through it during my last playthrough, not to mention tweaking some Papyrus scripts to my liking. I was doing so much picking and choosing that I just got fed up and extracted some BSAs and started mixing and matching models.
This time around I'm using Mod Organizer (more straightforward than Wrye Bash, more powerful than Nexus Mod Manager) and the experience has been much more positive. The way that it installs mods is bloody brilliant, to the point that I wondered why in the hell they seemed to be the first to implement it. I was actually considering writing a quick and dirty mod manager that used their approach* until I ended up finding it since I tend to deal with loose files in a lot of cases (especially texture replacers, since loose files are more efficient than BSAs).
And yeah, I use SKSE. It's pretty much mandatory if you want to have any fun (even with vanilla! I can't imagine playing without SkyUI).
*Basically, it installs the mod into a directory in its own directory tree. When it comes time to install the mod to your Skyrim/Oblivion/Fallout/whatever directory, copies the files over there. When it needs to uninstall or check to see if another mod is trying to trample on another mod's files, it uses the directory tree that it created to know which files each mod uses. Simple, effective, and it eliminates the biggest issue that NMM has when you need to uninstall and reinstall mods: namely having to wait ages for it to unpack 7-Zip files and doing the install progress all over again. The fact that it's compatible with both FOMOD and BAIN installers (unlike NMM and Wrye Bash, which don't really support each other at all) in addition to simple archives is a huge plus as well.
