There's no transmission output speed sensor, it's calculated based on the sensors.
There is a CAN line between the ABS module and the ECU, I would check if that is still ok.
You can find the factory manual here:
http://colorado4wheel.com/manuals/Jeep/WJ/
Schematics are included.
Can you access the ABS module in WJDiagPro?
Some info regarding the ABS to ECU wiring is also here:
https://jeepswj.com/axle-swap/