Your best bet is to find a local tuner that has powrtuner. If not someone with hptuners, have to buy credits with that though. If they flash a stock file onto the pcm and it doesn't resolve anything, let the trans shop know that. It may be their doing or a TC issue, I would post up a video in the trans section of what it's doing or send it to dave @ TEP to see if someone can offer more insight. If it actually is the shops doing, then they may want you to go to the dealer and have them flash it regardless, but i wouldn't do it unless they say they will pay for it if the problem is still there.
If that isn't working, I would find another compatible junkyard pcm and install that, if anything you can still keep the dhp 1.0 pcm or have a spare to send to reptile or someone to flash.
