Don't bother fixing the stud, you can just file down or cut a little bit off the tip of the shifter mounting screw to shorten it. Much easier to do, and there's plenty of replacements out there if, for some reason, you ever need an original length screw for the shifter.
Tip: put a proper sized nut on the screw before you file or cut it. You can the de-burr/clean out the threads at the cut by simply screwing the nut off.