Sorry I haven't updated in awhile.
After extensive wiring checks, ended up sending the PCM back to FS1 and they admitted they didn't program it right. They had it for 2 weeks. Installed again and the shifting problem was fixed. However, I was getting a misfire on #5 cylinder, lean O2 bank faults, and idle was low and erratic. Thought I got the misfire fixed with a plug change. Advice on the F150 forum pointed to possible clogged cats for the idle.
The pickup was drivable, in fact used it to tow my cargo trailer with 2500 lbs of wheelers in it. Did well on an 80 mile round trip. Hoped it would clear the cats out but instead the misfire fault came back. More troubleshooting found nothing. The manual said if the injector and plug are good (they are), a misfire with lean O2 symptoms means its a PCM problem. Arragh!
FS1 agreed and they have the PCM again. Hopefully, third time is the charm.