Did you check to see if the gear ratios were the same? Are you using the same torque converter or the one from the different transmission? If you installed a transmission with a lower gear ratio ie..... your GT came with a 3.29 overall ratio, and if you installed a transmission with a 3.05, 2.93, or 2.86 ratio then the torque converter will be working harder during each shift and the rpms wont noticably drop as much as with the 3.29 gear. Do you have the ID tag codes from each trans? I added a link to my website to find the ID code if you want to check
