+1 to launching with SKSE, and to avoiding the Steam Workshop.
I've used NMM since the beginning and have had no problems with it.
With regards to the textures not showing, this might be worth a try:
Go to Documents/My Games/Skyrim and open Skyrim.ini with WordPad/NotePad. Look for the [ARCHIVE] section, and if you see bInvalidateOlderFiles=0, change the 0 to a 1. Alternatively you can delete the line but changing it might be just as easy.
This was an issue with some of the body textures a while back, might work for this as well.
Another approach might be to disable all of the texture mods you've put on, and then bring them in one at a time. Enable one, go in game and check if it is working or not, then try another. Establish what is working or not, at least you will have a baseline to work from.
Good luck, sometimes getting a mod to work is trial and error.
Cheers,