All I can suggest is put all those parts back together and observe while moving rod up and down through the access cover as before. That 1/2″ slop has to be coming from somewhere. Yeah, straighten that rod, but I doubt that is the problem.

When you take the gear case apart, scrutinize the shift fork very carefully. Think, “How would I have shaped this, if I had designed it?” Sometimes they get bent a great deal, although the bend is so even and subtle on both sides that it looks like maybe it should be that way, on purpose. Judging by the abuse your upper shift shaft has taken, the fork could also be a casualty. I have been able to straighten them out; but they should be pretty readily available, too.

It just doesn’t seem like there is that much slop in the shift/rod/connector/bellcrank…. Does your gearcase have a shift fork pivot screw, or does it have the pivot shaft inside the skeg?
I guess at this point, I would pull the gearcase off and try shifting it by just moving the shift rod up and down to see if it shifts properly that way….
Again, you mentioned mixing parts from different years, I would investigate the part numbers of the items you interchanged to make sure they didn’t change between the two years. The only other thing I see is a potential problem in your top picture. The little hole in the bellcrank seems to be elongated a bit, which will add some slop where the pivot pin goes through…You seem to indicate there is no slop there though….While the powerhead is off, I would certainly update the bellcrank if the part numbers have changed…

Well, you found the problem and I guarantee you’ll never do it again. AND all it cost you was some time. I’d call it a win, overall.