I don't believe that you should have to worry about the transmission, but more testing will confirm that. I don't recommend grabbing the output yoke while it is running, just in case!!
And are you talking about the cable itself? Or the nut for the housing?
The cable just would need a little twist as it's square, to line up.
The nut for the housing can be a challenge for your patience as it's ine of the last things when you're ready to be done, and the grease makes it a bitch! Some cleaner and scrubbing should help. It could have been cross-threaded once in the past, so getting it right could be a big challenge.