FWIW (and not having done it myself) I can't see any reason why you can't keep the original ecu for auto box control but have another running the engine.
Basically, old ECU keeps all its original inputs, still has output to the suto box, but you disconnect all the outputs to the engine.
Give the new ECU all the inputs and all the engine outputs.
In theory, job done.
Only complication is working out what each input/output is (if you don't have a wiring diagram) and if the ECU gets upset when it tries to adjust an output, but doesn't see an expected resulting change in an input... The latter is what is difficult to predict in advance - probably not going to be an issue, but might be.
For example on the last one... I had a CX go mental on idle control, just because I disconnected the feed from the fuel pump relay to the fuel pump and instead wired the fuel pump straight to the battery (this was part of fault finding an intermittent non-runner*).

Who the hell would have seen that result coming?!
*I think I have finally found the cause to this, in November last year, about 15 years after I started!
)