I’m almost certain it’s just a valve body gasket
You replaced the VB? I was going to suggest maybe you have worn servo bores. I have a 2007 4.0 with the 5r55 trans, had I had it rebuilt at 80k. I'm only at 117k and I'm starting to get delayed shifts between 1st to 2nd and then 2nd to 3rd again. Everything else shifts and works fine and I never get any codes. The only thing I can think of for me is worn or wearing servo bores. I'm going to try the Aj1e superior solutions servo bore fix which is a servo that they've reengineered to regulate the pressure of the ATF fluid between shifts. This sounds similar to your problem and I think Aj1e makes servos for your transmission as well. Might be worth a try if the VB fix doesn't stick. About 18k after my trans rebuild I started getting bad shift flares again and they replaced my VB, that lasted about 5k mi and then I got minor shift flares again. It's since gotten worse but that might be because I put bigger tires than stock on it. I've since ordered a sct x4 ford flash programmer to adjust for my tire size to help with limiting wear and tear on the transmission. Anyway I hope your problem is solved.
I should say it seized up on me in a parking lot wouldn’t go backwards like the e-brake was on
