Neovalen, I just registered so I could post a THANK YOU! for putting together such a comprehensive guide. It was relatively easy to walk through, and, for a newbie such as myself, the guide gave me the chance to dig into tools such as TES5Edit and SKSE (which were a bit intimidating) that I never messed with before.
I do have one question. Although I am now familiar enough to go into these tools and follow your instructions to edit a mod, I'm wondering how I would go about learning WHY you know to edit a mod in the first place. For example, taking the first mod in your list that requires cleaning... (Yngol Barrow Button Fix). Before I follow your steps and go and clean it (naturally, I've already done so, but pretend I have not), what do I click on/load up to see that it, in fact, NEEDS cleaning? The same would go for a mod that "does not carry forward changes from Dawnguard.esm" or "wild edits", etc.
How would I know that a random mod (one that is not in your guide-- Ultimate Follower Overhaul, for example) requires any of those same changes/edits?