Have a read of this:
https://old.reddit.com/r/xcom2mods/wiki/mod_troubleshooting

I've never had that problem. I'd suggest trying a binary search, if the basics like user config. clearing don't help.

@Dragon32
I've regenerated the config, seems to have actually updated mods that had not worked previously but still have the issue, still working out the kinks. Will update on progress later.

@Dragon32
I went through all the options an nothing but regenerated config really helped do anything that was remotely helpful(or could be done), My game has not run'd smoother in years. The framerate smoothing is already turned off by default by a mod everybody uses so I can't do that, I guess I'd have to play and rank up a soldier past squadie to find out, but I have a feeling the moment I try I cant chose anything just like promoting the rookie.

OK. Good luck.

If the classes was messed up, you need to rebuild the soldiers via console or start a new game.

UPDATE
I'm going to just do the most painstaking thing possible and just start from 0 and go up by Quality and UI an then some, cause if it's somehow nothing, I'm gonna go crazy and just uninstall and reinstall, and if that doesn't work, I'm open to suggestions after.
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God I hate everything ༼ つ ಥ_ಥ ༽つ