2011 LML throwing codes and stuck in limp mode.

Sorry I'm not 100% sure where to post this. I have a 2011 LML crew cab long bed SRW, 60k miles. It's my daily driver, but my husband's realm of expertise not mine. I was on the highway, and after a rest stop it dropped into limp mode with no warning. The check engine light came on but it wouldn't tell me anything. It was in third gear, I pulled it off the highway. The indicator for which gear I was in disappeared. Made it up to the dealership. They told me it was a detent switch in the transmission, and cv boot. My husband had me bring it home since that dealership is shady and we didn't trust their work. RPM's were up to 2500 to 3000 just to get up to 45 mph, shifting rough like it was having a hard time deciding what it should be in, no light to indicate what gear it was in.

Husband drove it to just get the codes read, and it threw itself into neutral while he was driving. The transmission was overheated from the smell it seemed. On his bosses advice he disconnected the battery, reset the code long enough to get back to the house. Long story short it just had a new ATS stage 1 Allison and torque converter put in. We picked it up from the transmission shop and the check engine light was off, but my husband had the same issue after he pulled out. He drove it back, took the tech for a test drive and they hooked it up to run some sort of diagnostic on the transmission. He said it came back fine and the issue wasn't with the transmission. It went into 3rd gear again halfway home. It's been in our driveway ever since. I have no idea what I'm dealing with here, and my husband isn't much help with his work schedule right now. Any ideas what it might be? I love the hell out of this truck, but this is getting old. Oil was changed five months ago and looks okay with truck reading 30% oil life, nothing leaking, air filter replaced with stock two months back. Entire truck is stock except the new transmission, pan and torque converter. Something I read mentioned maybe a mass air flow filter? Any help is greatly appreciated!

Why was the trans bad in the first place? Was the original unit abused?

The limp mode that you are experiencing sure sounds like a transmission limp mode. I've not been a fan of ATS trans stuff for some time now and it sounds like this is related to the trans job. There should sure be a DTC set someplace.

Oh wait let me clarify real quick, I didn't word that right. So it went into limp mode on the highway, made it home after the dealership, went into neutral taking it to the AutoZone to read the codes again. Then ordered the new transmission (we were already planning on it since we were going to put mods on it, so decided to bite the bullet and do it now. Maybe stupid, but it's our first diesel and it's a learning curve as we are young dumb adults lol.) New transmission was put in and then still had the same problems. Haven't had the codes read again yet.

As far as I know the original trans wasn't abused. We've had it a year and a half, we treat it pretty well, the most we've done is a 4k mile trip with about 6,000 lb behind it. Before that from what I could tell from the stickers and wear it was a oil slope truck up in Prudhoe bay.

We've seen plenty of grief from the TCM, but that is not something that I hear about occurring while driving and there is often a communication code that points to it.