Update on that Commander Transmission, well it's kaput. It was still shifting smoothly, but I think the pump has started to fail. Dropped the pan today, fluid was off color, only a year old with maybe 20k driven since we found the pieces in in the pan. A lot of fine metallic debris, silver rivers in the redish fluid, no big pieces just the fine shavings of selfdestruction. I think the filter was starting to get clogged by it as well.
Before dropping the pan we noticed a few occasion where the transmission seemed to lack power or fell like it was searching for first gear. Never actually sipped in gear, once it was going it felt ok and shifted smoothly. It would be a hiccup you could almost ignore.
Reading about NAG1 transmission pump failures it seems a likely cause, also started getting nosier when warm. Already had a low mileage replacement on hand started taking the jeep apart today. Out of all the things I've done to this jeep I never had the drive shafts off for any of it including replacing the starter and replacing the engine. The front CV prop shaft was a PITA to knock lose after all the bolts were out.
Not exactly a KJ problem but if anyone is in a similar situation finding substantial pieces of needle bearings and such in the oil pain, you can get a little more use out of the transmission if it was driving ok before you found the debris.
Thanks to all for their advice! Over two years later turns out we did ok with it, I was prepared to pull this transmission and was on the lookout for warning signs. We didn't get stuck, and it's home where I can work on it.
BTW that 3.7 out of the 2012 Liberty we swapped in has been perfect.