I've pretty much not re-installed Skyrim once since I first put it on my machine in 2012. I've modded it quite extensively, and usually been pretty careful with it but a lot of it has been a learning experience for me, I use the Nexus Mod Manager to install everything, even mods from other sources I load through it. I used BOSS (now LOOT) to sort them, and used Wrye Bash and TES5Edit to fix conflicts and dirty edits, even then I don't consider myself an "expert" on this whole modding thing. Anyway I've had my fair share of issues with the game over time and have resolved most but at this point there's issues I just can't seem to figure out how to resolve like http://imgur.com/7SQ9Rfr.
I have close to the cap on the number of mods running, and while I don't want to necessarily keep "all of them" I do have a list of about 150 or so I want to get.
So I am thinking my best solution is to do a completely CLEAN INSTALL on Skyrim and all related folders and download everything fresh, mods included. So a couple of questions:
1) After "uninstalling Skyrim" what folders on my PC should I ensure I delete to make sure nothing is left? I know Skyrim puts files outside the install directory and I don't want residual files gumming up my new install.
2) What steps should I take when installing such a large number of mods concurrently to hopefully not break anything? Most of the mods I am installing I've already confirmed work in-game (possibly with some cleaning involved) and don't have any conflicts I've found thus far, but I don't fancy going the "install one mod > test > install another mod > test" route for 150 mods I already know I want.
3) Is Nexus Mod Manager the best way to install mods? I like being able to just "disable" a mod and have it remove everything from the associated data files folders without having to manually go in and figure out what goes where and what a certain mod added, but I'm not sure if my assumption of how well it works is true of how it works.
4) Mod compatibility has never been my strong point. I install a lot of companion and clothing mods that don't always use the same "base body" mesh and I'm afraid that's what probably caused my body mesh issues (the one pictured is a minor one, sometimes the texture stretches out infinitely and fills the whole screen when I look at the person (it's usually certain armors). Any tips to make sure my companions, chosen base body mesh, and clothing collections all get along?
5) Any other tips would be appreciated to help make this go well. I haven't played Skyrim in months because this job ahead of me is so daunting and I know it'll take several hours to get to where I want it.