No shift, engine miss, and crazy tach!

[OKGMC4]

I dropped the truck off at the tuners place a couple days ago to get the ecm worked over and he calls me last night and says everything went pretty good up until the end where he says it won't shift past second gear, has developed an engine miss at 5200rpm, and he wants to know why my tach shows idle at 1500 and redline at 8000 rpm. The truck has never done these things before, and certainly not in the same day. He's telling me the trans must be shot and it needs a $900 rebuild. Could this be a bad ecm or ground issue? I need to go look at it but I just can't imagine all these things (that are ecm related) happing at one time on a 5.3/4L60E with 65k on it. Any thoughts?