Once you swap the valve control body from the 01/02 into the tranny, it comes with the wiring harness so everything connects as it was before. I hope this answers your question. The link provided gives all the info.
Can't help you with which Sequoia transmissions would work, but I can tell you what I learned during my 2WD to 4WD conversion on my 2001. I couldn't find a good 01/02 version, but I was able to swap the internal valve body from my bad 01 transmission into my 'new to me' 98 version.
The 96-00...
Glad to hear that you're still making them. I would like a set in black. I'll try to reach out to you via PM. I'm new to the board so I'll see what I can do...