I know you said the linkage was "a-ok" but I tend to focus on the very simple things first, otherwise I tend to complicate things and end up buying parts I don't need, or paying Mechanics I don't need to.
Did you just see that the linkage was all there.....or did you actually get under it and watch it whole someone else tried to shift it?
Also detach the linkage and see if you can shift it by hand.
Is this a hard lickage or a cable linkage?
Does the trans shift lever move through all the spots or is it frozen in reverse?