This isn't intended to sound smart-assed, but: You did back up the mod, right?
As far as I remember, GECK actually creates a backup of your esp every time you press the save button. It should be placed in the
Data/Backup folder.
I can even start a new game even after deleting my setup folder in my documents and fallout3edit detects no error
You mean that you can only start a new game after deleting the
My Documents/My Games/Fallout3 folder? Or that you can start a new game, but not load an old one?
If the latter is true, then tinkering with the mod likely foobared the save. Try to load an older save (preferably from before you started the mod) and see if it loads.
Finally, which version of Fallout 3 are you using? Before the 1.5 patch, removing a mod that added a perk would cause the game to crash when loading a game if the player had the mod.