You would need a manual computer and a
tranny from a 99+ being that we have an electronic speedo sensor. You could swap the sensor. There is a writeup on V6power.net on how to do it. Bear in mind, you will throw codes because it is looking for an auto unless you change the harness.
I don't think you can get a 3650 bellhousing, but don't quote me.
I would upgrade the auto with a J-mod and call it a day. It's just less headache, and much, much cheaper......
If you get a T5, get an '01+ they were better
tranny's......