They are different engines. The 04- Tacoma is the 3RZ-fe 2.7L and the 05+ is the 2TR-fe 2.7L. The 2TR has variable valve timing on the intake. I dont know what the difference in the bell housing bolt patterns are, or the transfer case. They are similarly configured in the engine bay but ??????
If you want a manual control case with your current transmission you can use a FJ Cruiser manual case. It is the same case with a lever.