The obd2 ECU has the TCU integrated within it, so you would just need to give it the inputs it's asking for and could probably just abandon the outputs. Might throw a trans code but who cares since the trans is controlled independently. Worse case you could build a digital transmission with an arduino and some code to give the ECU something to 'control'.
This topic was hashed out pretty well back in 2016 when a few of the members were doing 5 spd manual swaps into the US spec J80's. If Toyota had ever shipped a M/T J80 to the US, this would be easy, just put in a M/T ECU. But, they never did that. A bunch of offshore M/T ECU's were investigated and some tried. Problem was that Japan, Australia, middle East did not get OBDII until much later. The European J80's had just one O2 sensor. A straight M/T ECU swap did not work to keep OBDII functionality. You could swap an offshore M/T ECU and get rid of the check engine light.
There was a bit of digging into the US spec integrated ECU/TCU and the biggest hurdle was:
"The problem would be that the ECU won't do any of it's magic as far as readiness tests and open/closed loop without the VSS signal. With the VSS signal, it expects to see certain things happen when it tells the transmission to shift which would be impossible to simulate because of the real world (engine RPM can't be simulated, the ECU knows the real value)."
Quoted from sbman, on page 9 of the thread:
I evaluated the EWD in relation to the auto trans. It does not have very many connections. I can see that wiring the 'N' indicator to light up won't do anything because the ECU doesn't even detect this signal. I do believe I could design a circuit to emulate the transmission and make the ECU...
forum.ih8mud.com
If you live somewhere that does not do biannual smog checks, you can deal with the code. But, if you do live some where that requires biannual smog, then you may need to have the check engine light off, as some states require that the light is off, even if it is a transmission related code.
There is a Supra transmission emulator out there, but that was designed for the 2JZ-GE engines with VVT, when doing a manual swap. On those cars, with the stock transmission missing, the computer went into safe mode and disabled the VVT functionality, taking away some performance. As I read the pinout for that emulator, it would not address the issue with the J80 ECU/TCU.
Please follow link for information about the ATEMU and installation instructions. https://www.toyotav8.com/forum/devices-atemu-mpx-signal-converter-ect/31-atemu-information-and-installation-instructions
quantum-auto.com