It actually is lined up correct. I had no idea the two issues would be related. I just kind of expected one day to have to crawl under and look for something near the tranny to deal with the shifter.
I can't believe I spent months of intermittent "getting-outta-my-truck-with-a-screwdriver" so I could start it and it took 30 seconds to fix. *facepalm*
Much respect, Alan.