a RE4R01A is a frontier transmission. As we all know the job of any transmission is to multiply torque at relatively low speed to transfer power and then obtain a direct or overdrive gear at high speeds to the input shaft turns slower than the output shaft. Robert, I believe these transmissions use the ECM to control shifting by using engine sensor voltage inputs such as TPS, MAF, MAP, CKP, ECT etc. The voltage signals from the engine sensors is used to detect engine speed and load. The ECM then energizes shift solenoids to control shift valves in the valve body, opening passages and directing pressurized fluid to certain clutch packs to obtain the gear ratio to match engine speed. If you were to run a separate transmission controller, then yes wire it to the ECM to control shifting. As for the shift linkage having contacts instead of levers, I dont know how that could be adapted because the shift linkage directly controls the manual valve inside the valve body.
Hope this was of some help. B)