Of all things you mentioned only NPCs with shield stuck to draw weapons is known and common bug, and yes, Dual Sheath Redux causes it. I only once heard about female feet bug - someone mentioned it on rutracker. Never experienced it myself. Does it happen in specific times or they always have weird feet?
Feet bug must be related to skeleton. Unvisible headpieces bug I bet is because of wrong load order since I had it before release and fixed it changing load order of some mods towards the end of list.
Seems there are some inconsistencies, loadorder.txt and plugins.txt have differences, some mods aren't there for example. But I guess it doesn't matter? If I remember correctly loadorder.txt is taken into account if you run the game from some program like NMM. Plugins is the one that's actually taken into account if you run the game by launcher or skse. In any case, I was careless with a few things, and I shouldn't be messing with files when not completely sober after new years eve, I actually managed to fuck up the game, not any saves or cloud to salvage the situation, so fuck it, I was thinking of starting over after I was done with the imperial campaign anyway. So, I re-installed the package, this time I went with light load order because I felt the game struggling with all the scripts from time to time before. Went inside, and checked a few things with the console, females corpses still have the bugged feet, also did "help eyepatch" and added a few of them, the plain "Eyepatch" appeared on the char but it was further off from the eye, wasn't sitting correctly on the head, also tried some of the other items that I remember were missing like Ritual Shroud of Boethiah and Tribunal masks were some, and it seems it's mostly stuff like that with weird socket rules, masks, capes etc. that are missing mostly.
Do you have any idea on where I could start to fix any of those problems? Since reinstalling and double and triple checking load orders doesn't seem to be the issue. Which mods should I re-install for example to fix the bugged skeleton? xp32 and the one that changes idle stance I guess... I remember having problems with skeletons back when I modded skyrim, so I don't know if it's worth messing around with your package just for something so small, but if you think any of these problems could be fixed easily please let me know and I'll try it. I'll post the 'light order' just in case it's different from the one you used that you had no problems with as you said. If you still have the order around and could compare it would be nice.
Oh and happy new year to everyone here!
EDIT: Lol, actually managed to fix the skeleton issue, I started small.. all I did was download realistic ragdolls and force - realistic, then replace the old skeleton_female.nif and skeletonBeast_female.nif with the ones from realistic. There was a difference in file size. Do you think this is going to have any unforeseen consequences? Hopefully nothing will get fucked up, like combat animations etc. Idle seems to be fine, as in, the immersive ones from the mod are in place. As far as I can tell the only problem I see is the missing textures. Oh, also the SMC deal, unfortunately if I run the game with it the game stutters A LOT, like there's something seriously wrong, even indoors when fps is stuck at 40. Is there any way to make it work, or should I stick with skse? Guess I'll just have to restart the game every couple of hours to avoid CTD's.