I have been fighting this problem since October.

I lost my Alternator while taking the kids to Gymnastics back then. I tried to make it back home on the hwy from across town (30 min)
I drove till I lost dash nights and I started to loose the fuel pump.
I called it quits, coasted to a safe spot to wait for the wife.
I could hear relays chatter as I waited

I replaced my alternator a few days later. Truck still had a "check charging system" warning.
I used my SCT to reset the KAM (Keep alive memory)
check charging system problem is gone.
but now! now i have......
NO second gear.

I replaced my valve body after a ton of reading
I replaced my EPC today

if i drive my truck hard, like 3/4 throttle or more < it shifts perfectly.
when its cold, and I leave home it shifts perfectly at any throttle position.

when I am at full operating temp and drive like an old man, it neutrals in 2nd.
I can manually shift to 2nd and it work perfectly.
Its like I have a leak at operating temp.

I know that the EPC would have been at max pressure with my dead battery on the way home at 100 kph
did i blow out an oring?
what's next?

Thanks!