Problem is, when you Spawn in front of Vault 101 with no equipment or quests, then you have a corrupted save. No matter what caused it. The only recourse is to load an earlier save. Reloading the existing save, even without the mod that you think caused this will not fix this. There are no utilities that will clean a save.
Few more tidbits, always, I mean always, even if everyone says it is a good mod, make a forked save when loading any new mod. Never work off of an existing save. To further protect yourself, make the forked save before you even install the mod. The usual method of loading the last save after you have installed the mod and then creating a new Save Slot should be enough, but....
Having a Forked Save will allow you to load up a pre-mod save that should not have any issues from the mod you installed. Assuming you remove the offending mod.
The other reason saves corrupt, which also could be the issue here, is writing over the save slot too many times, loading an Autosave or Quicksave (which are not complete saves). To that end, I don't overwrite a save slot more than 5 to 10 times. I can always delete the extra ones, but I can not recover from a corrupted save.
interesting I didn't know that about F3 regarding showing up out of Vault 101.
I'm not sure about forked saves but I always make 3 saves with my working load order then add mods only to one of those saves (with a new save) then after testing and such may go back and delete at least one of the older saves. Each character with Oblivion and F3 have hundreds of saves.
If it is an OBSE plugin then it may have created a file somewhere of perhaps it overwrote an F3 component.
I have a hard time believing the OP came here to ask for help but no posts on Nexus??? I'd go to the source first.