Your problem is that the HD transmission has a different overall gear ratio of 2.93:1, your GT trans has 3.29:1 gearing. You need custom pcm tuning to correct your problem. If you or your transmission guy has a scanner you will find that by looking at the "Current Gear Ratio" info it will read .88 in 3rd gear. It MUST read 1.00 give or take .01 to work properly or it WILL throw an incorrect gear ratio code. When this happens you will have very harsh shifts as the pressure is maxed under most conditions and lockup comes on very hard all the time which is hard on the trans. The gearing changes is made by changing the drive and driven chain sprockets inside the transmission and requires taking the transmission half way apart to do this so its a pretty involving task. Having the pcm reprogrammed will take care of this. There are other ways to get around this but reprogramming the pcm is cheaper and easier to do.
