I doubt that but that is really odd how it started doing it just with the short throw shifter.
even with it hitting the plate it shouldn't cause a grind, when you unhook the shifter from the trans your stick can spin around anywhere so there's no guides in there to make sure it hits the right gear it's all in the trans you know? not sure how to explain it fully. shifter is just your way of changing gears if it's long sort crooked anything if you can use it the trans will work. I made my own short throw shifter I cut the ball out of my stock one and flipped it so the longer part was on the bottom and put some bolts in it and welded the snot outta it, now I got one mean short throw that's angled back and to my leg instead of the passenger knee knocker.
the only thing I can think of the shifter hitting the back of the mount is it isn't fully engaging in 2nd gear that would cause a grind because the gears aren't meshed together all the way. also a good way to strip gears ha ha.
what I would do at this point is when you get the time put your stock shifter back in and see what happens man. also check your fluid level in the trans make sure that's all good, and if the fluid is dirty change it, clean fluid will keep the trans happy!