well from the sounds of things so far my only advice is don't let your mechanic make these disisions for you anymore, you have to tell him you want to use your original ecm/pcm which ever that was in the truck when you brought it to him, and that you will get any and all tuning needs addressed by bill with yout gryphon, all he should be doing at this point is the wrench work i would suggest as soon as you hear it fire up , drive it QUICKLY out of this guys garage before he starts attempting anything else that may affect the drivability issues before you get the tuner installed , best of luck , as for bill all he needed from me was the pcm/ecm which ever lol number that he told you about earlier from your existing hardware that was in the vehicle as well as a list of any other mods you have done past stock stage with this vehicle , ie, change of muffler diameter pipe, removal of the cats that sort of thing and the year and size of the newly swapped engineor as well the original tranny if you haven't changed it , unless it is in bad shape i would leave your original tranny alone as well, the tunes will fix any shifting point issues and torque conversion.
good luck, feel free to pm directly if you have any other issues, all these replies to posts and pms go directly to my blackberry and i uselly just respond via the cell phone as i was doing today with these ones from my job site
benifits of being the boss lol