If you had the harness modified by Dynatech Motorsports I feel for you. Those guys appearantly know nothing about LS1 type engine/transmission conversions. I would get a wiring schematic for the pcm in the truck and verify all the pinout and sensor connections. I hear day in/day out of them screwing up the pinout configuration on the pcms. Dynatech is starting to realize they don't know crap about the LS1 types and no longer do the LS1 type conversions. Do a web search on "Dynatech Motorsports" and you will find pages of people dissatisfied with their piss-poor work. They lack the knowledge and tools to reprogram the PCM correctly. I would suggest you contact Allen/Farmtruck and have him reprogram your PCM correctly before you change your transmission. Allen has a "Light" version of his programming services that is reasonably price.