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 versions use a throttle cable. The 01/02 versions use a solenoid for line pressure control instead of a cable. When you swap the internal valve body into the pre ‘01 transmissions, it converts them into the 01/02 electronic version. Finding a 96-00 transmission is way easier!
The following link describes it all:
Converting 95-02 Auto Transmission to 03-04 | Tacoma World
Hope this helps.