Doing a swap from auto to manual on my rig and I just discovered ( I thought how did I miss this ) my transfer case has different part number between auto and manual transmission per numerous Toyota parts sites - so what is the issue with my original transfer case and the difficulty it seems to find the version for the manual configuration

 

There are some different types. Multi-mode, j-shift, pushbutton 4WD, etc. What kind do you have?

I have a manual '99, it had a J-shift. When I put a doubler on it I got two donor J-shift cases (so I could assemble the doubler on a case before taking my truck apart) I was able to get compatible j-shifts from automatic cars.