OP, the ECU part number you want is 89661-3D590, but they are very difficult to find. This is the one I have, I found mine through another member who found one in a salvage yard. Other ECUs might work, like the 2000 model year 89666-35160, from what I understand everything powertrain-wise is exactly the same and the ECU pin connectors are the same so it should work, but 89661-3D590 is a sure bet.

There was no CA spec 1999 Tacoma, but there was a CA spec 2000 Tacoma, and the ECU part number is 89661-04670. If you look at the pin connectors on the ECU, the connectors are all the same except the middle connector, which is missing from the Tacoma ECU. All the wires that ran off that middle connector are for an immobilizer system, so if your 4Runner came with the factory immobilizer then this ECU will NOT work, but if you don’t have the factory immobilizer I don’t see why this ECU wouldn’t work.

After all this, you CAN run with your A/T ECU and it’ll drive just fine but with a CEL, and just keep your eyes peeled for the proper ECU before you do a smog check...one will pop up for sale every once-in-a-while.