Humm, don't just re-install.
The best thing to do here is doing a good uninstall, reinstall and verify.
I would hold off on the F4SE for now, being you are crashing in the pre-war.
This is a good video as it touches on the uninstall part.
Also, for some folks, the quick start stuff works fine.
I fall back to someone smarter than me saying that the Base Game is still running set-up/start-up scripts even after the meeting with codsworth. It can be a dice roll how everything else in a LO interacts when something is different than the base game.
My advice is:
1. Only a few mods need to be installed at the start of a game save. Many can wait.
2. Make your own quick start. Make some unmodded saves at least to the point of leaving the vault. Then copy them somewhere safe.
If you want to start somewhere else then use unmodded saves to that point and use COC or tmm1 "I like tmm1" make a hard save there and "bam" quick start to any future game. Console in whatever gear you want to start with or stat changes after that.
Use that save to start your future games and then mod away. At least you won't be replaying everything.
SS2 isn't like SS1, you can install it after leaving the vault.
Oh. hahahaha, make a choice about the UFO4 patch, just never uninstall it.
If testing for an author, then I ask, and normally don't use it.
I always use it when making a new save-file for my own games. That is the one mod that gets baked into a new save file.