I think drivability issues have a lot to do with the base PCM program. My buddy did the auto to manual swap with no issues using the auto PCM. His cruise and backup lights worked, have to enable cruise through the clutch and brake and the backup lights work with using the factory stick transmission harness to the backup switch (2 wires) on the 5-speed. It helped that he had the entire donor truck to do a factory install of the 5-speed down to the blank out panel for the shifter indicator in the dash and the 5-speed transmission doghouse. Auto out and 5-speed in per the Service Manual plus a couple of jumpers.