Not sure what other inputs the trans gives to the ECU (but I guess you can find out since it sounds like you have the WS manual), but its not possible to simply plug in the Gear selector switch (it was a smallish box in the 97LE) back into the remaining auto loom, set it at the appropriate gear (1st I guess), and then secure it somewhere ?
Like ignition suggested, it might be easier to kludge some sensors / inputs back into onto the auto transmission loom, than fiddle with smartlock and other ECU's.
Just for interests sake, the EL manual computer plugged in and worked 1st go with on the EL - BUT I can no longer get the car into the idle self test mode
Not sure if this is related, or something else thats freaked out since I last checked timing... (will experiment this arvo - weather permitting).
At least you've managed to nail down your problems to a specific cause though (unlike myself, who is still floundering around
). Let us know how it progresses...