Mods stopped working after updating MO

[DarthFalcon]

I was previously using Mod Organizer Alpha 2, and decided to upgrade to Alpha 4. I chose the install option that would let it handle multiple games, installing it in the AppData folder. I manually moved my installed mods/downloads from Alpha 2 to the new Alpha 4 folders, and now none of my mods work properly. I have triple checked every ini, they are all configured properly, and none of them are set to be read only. I've also triple checked the inis via the MO's built in ini editor, those look fine as well. The mods appear in game to an extent, but all of the textures/meshes are either purple or non-existant. My main menu theme replacer doesn't even work, and a full reinstall of Fallout 4 is not really an option right now because our ISP has gone insane with data usage restrictions. A few specific examples of mods that don't work: I have a main menu theme replacer that doesn't replace the main theme, I have a modded scope attached to my gun that isn't there, but hasn't been removed either as I have no iron sights, the clothing I was wearing is still in my inventory but is invisible in game (I forget which specific mod, it's one of Eli's sleeveless outfits), and I'm using CBBE but have no body, in third person it's invisible and in first person my hands/arms are purple. Any ideas? I'd rather not try NMM as I strongly prefer the ease of use Mod Organizer offers, especially when dealing with mod conflicts.

 

EDIT: Just to confirm that it was an issue with my mod installation and not MO, I downloaded a single mod (the main menu theme replacer) and installed it with NMM, still not working.