As long as you have a properly setup TurboLamik TCU (the main one I have seen for the 8HP, there may be others) to “replace” the stock unit I see no issue.I wonder how the stock ecu will act with out a transmission connected.
When swapping Supras from a similar auto to R154s etc it was an easy as switching the box, adding a pedal/master and slave, and re-wiring the neutral safety switch. Most of the JZ swaps I’ve done ran on a stock auto ECU; on these older Toyotas that don’t have CANbus systems they’re not heavily integrated.
It would be cool being able to rev-match a 2UZ when braking down steep grades, or hold a gear up I70 towards the tunnel without having to absolutely finesse the skinny pedal