What a pain in the A$&, but thats part of the reason I went with a built C-4 in mine. I originally planned to go with the AOD for the overdrive, and have a manual valvebody and upgraded input shaft, but get this, I call the company to place my order, and whom I've spoken to 3 times before over the phone explaining what I needed, and he tells me the AOD will have no compression braking with the the manual valvebody intalled. WHAT!! at least he told me before not after I sent him the check. The C-4 or C-6 doesn't have any computer inputs, and removes the problems of the calibration numbers not being correct. So you can run a ECU for either a manual or auto trans with no problems. It just comes down to doing your homework, and from the people I have talked to over the past year who have done the swap many times, the BAR referees (in San diego at least,) are will go out of their way to help you complete the swap properly.