Swapping out the throttle body could be causing the car to run real lean/rich. This program you have installed, does it take into account the new TB? I know with my car, if I change anything with the air intake or exhaust, I need to get the Air Fuel ratio rechecked and/or corrected. A throttle body change could have a huge difference on how much air you bring in. If the car doesn't know what to do with that much air, it could become unhappy.
By the way, I am by no means a motor head. I am just stating things I have learned since buying my cobra.