I'm disappointed. I thought Joe was the "sheet metal surgeon". Joe, how come you keep coming up with practical solutions backed by years of experience and refuse to commit to irresponsible hacking of Jeeps in pursuit of half a$$ed repairs?
With a manual if you can get it in gear it will work, unlike an auto.
I know about having a good shifting transmission after wrangling a worn out box, done that a few times myself.
EDIT: Getting old--I don't know if there was such a thing, but maybe you got a new box with slightly different gearing in it, that would make it perform differently.