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I would also "verify game files" via steam, which should delete any folders that contain mod related content from within the steam folders for your game.
Uninstalling doesn't automatically remove everything related to a game from your PC. You might need to uninstall and then find the related folders that remain and manually delete them.
https://help.steampowered.com/en/faqs/view/0C48-FCBD-DA71-93EB
Again, I will reinstate this...
I CANNOT ACCESS THE MODS THAT ARE FROM FO4 ITSELF!
I am a PC Gamer, I don't use Bethesda's In-Game Mod BS unless I have too, I have NexusMods for that. However I did have some Mods installed on FO4's Mod Menu and I cannot get access to it as my Post says. I'm asking if anyone else has had this issue as I'm now doing a 2nd Reinstall of FO4 to try and Brute Force the Mods from FO4's In-Game Mod Catagory out of FO4
Trying to understand your position.
So you're saying the the game thinks it has installed several mods from the in-game mod manager, which should be deleted, but apparently aren't?
Can you remove them from your boot order in the mod manager? If they don't boot, they shouldn't affect the game.
There may be different ways to deal with this, from making sure your internet is stable, waiting for bethesda to get its crap together, waiting for steam maintenance to finish, or wiping your manifest lists for the mods in your folders and getting the steam download cache cleared. I'd suggest finding the threads which have specific lists for such a problem because it is very common these days particularly after the next gen update.