If the pcm wasnt reprogrammed for the 3.05 gear ratio then there are going to be problems and the pcm will throw an incorrect gear ratio code and this causes rough shifts and odd tcc behavior. In your favor the gear ratio can be changed by using the differential out of your GT transmission in the new trans as long as it is still in good usable condition and that will take care of your gear ratio problem and may also help with how it feels but likely the trans you put in has a torque converter with a different stall speed than your original one and is making it feel a bit looser and you are seeing the rpm change not as much as before during the shifts.
