That's a good point about boosting. I've read you could probably do about 6psi since, as Zuffen mentioned, the 3uz rods are smaller than the 1uz rods. 6psi would still be a very significant performance increase compared to all our naturally aspirated options.
How about 3UZ-FE 5A/T tune? There are no JTAG contacts on the ECU 89661-50590, unlike the newer ECUs for 3UZ-FE 6A/T. I believe it can be flashed using OBD2 connection. But here might be a problems with reading stock firmware and with restoring ECU if something goes wrong while flashing.