I have an '82 30 HP with (pretty sure) the same shift shaft configuration. On mine, one turn off on the coupling nut doesn't cause a shifting error. What does happen in mine is that it will pop out of reverse when I'm fiddling around with it. If that happened, and you didn't notice, it might be the cause of the problem.
How about try this: un-do the mid-shaft coupling nut, make sure gear box and shifter lever are in sync, and, re-couple shift shaft making sure it doesn't pop out of gear? If necessary you can manipulate the lower shift shaft with pliers through the access port.