2016 pete 587 issue after ecm update

I took tgis truck to rush truck center to get my ac short fixed and they told me there was a recall on the ecm, that they had to update it....

On my first trip out I drove 600 miles and check engine light came on saying scr altered or fault detected death in 4 hours. So I drove for 1 hr to mephis dropped my trailer off at the receiver and took it to rush truck center to get it hooked up to a computer. As soon as I pulled up the lights turned off, so I figured I'd have them hook it up anyways in case it was something serious.
2 hours later they tell me there was an inactive code for a short detected in the dpf harness or something, that the tech looked at it and didint see anything so they sent me on my way. Im having a hard time believing he pulled the side panel off because everytime I went out there all I saw what a computer hooked and the truck doing a forced regen.

So I picked up my trailer got loaded and started driving to phoenix. 500 miles down the road just the check engine comes on no other warning or anything, so I stopped, turned the truck off for 10 mins while I look for a shop when I turn the truck back on the light is off.....

I called rush and they said its prob a glitch to not worry about it unless it stays on... now ive noticed if I turn the key on without starting the truck the turn the key off then to the on position again the check engine light does not come on at all during the startup test. Also my transmission will start beeping and when I put it on drive the truck shakes and revs up.

Does anybody know what the problem could be? Is it the ecm update cause ever since the truck has been doing all sorts of weird ####.....