Sorry to hear of your inconveniences. I don't know for sure, but I guess a good way to clear controller bindings manually is to find the config file, open it in notepad, and delete all the bindings there.
I am aware FNV supports the controller natively, but not well enough for my tastes. As with many games it just doesn't offer the customization PGP can give me. Switch buttons, and mouse sens altering buttons are key to my play style.
I also mentioned somewhere, but will again, you have to set your PN bindings to the ones I used for this to work, UNLESS you manually change the profile bindings to the SAME BINDINGS that PN uses in game. And you need to make a new save or PN forgets your bindings.
I think I had the hotkeys set up in a line for all the quick throw types
g h j k l ;
It's in there somewhere, take a look.