Redneck Truck

Not sure what metrics the ECU uses to determine the appropriate throttle position at any given time, but it seems like the signal from the gas pedal is the least important one. Sometimes, it'll rev to the sky with a blip of the gas pedal, and other times, I'll floor it in 2nd gear and it'll feel like I'm flooring it in 5th gear. There are no symptoms, I don't think it's a mechanical problem, and I would love to get it resolved - I've never had a vehicle that behaved this way, but this is my first swap car.

Does anybody know if different throttle programs or tables were used between automatic and manual cars? I'd love to install a regular, manual throttle body with a cable, but I'm sure the ECU would have something to say if I did that. Has anybody dealt with this issue?