manchevy

I have a '98 Camaro Z28 6-speed that I installed a different computer (from an automatic "98 Trans Am). Before I installed the motor in the car I ran it on a run stand with a stand alone harness and it ran fine. Now it is in the car with a car harness. I have EFI live. I removed the VATS. The car ran and seemed to be ok except for some weird codes for the automatic setup. It ran for 2 days and then it shut off. Now it will fire up but shuts off right away. It purges fuel. The calibration seems ok. I went through it with EFI live numerous times. I'd like to change the computer over to a 6 speed. Anyone know how to accomplish that? How do I get rid of the automatic codes? I've done the VAT relink and BCM relink. I changed the VIN for the car. I checked all grounds and fuses and relays. All seem ok. Any suggestions for what I need to try next? Is there anyone in Madison or Janesville, WI area that does EFI tuning that I could call and discuss this with?