Seems to me the flexplate was the same. I know I just replaced mine and the only question was internally balanced or external. They didn't seem to care what transmission it was hooked to.
If you check into it with the transmission people, I think you will find that your transfer case can be modified. They use the same chain and all, just the input shaft and rear seal change. Maybe it's different with the manual, but I remember it not being a big deal.
If you can get the pin out info, I think you could make the changes at the end of the harness that plugs into the ECM. You should not have to mess with both ends of the cable.
If you check into it with the transmission people, I think you will find that your transfer case can be modified. They use the same chain and all, just the input shaft and rear seal change. Maybe it's different with the manual, but I remember it not being a big deal.
If you can get the pin out info, I think you could make the changes at the end of the harness that plugs into the ECM. You should not have to mess with both ends of the cable.