This is an interesting idea. I think you might be able to do what you are saying. The early engines really did run as pretty much two different engines. If I remember correctly there are two crank sensors and cam sensors etc. Main thing would be if the firing order is correct and remember that the intake is swapped from ignition on the banks. So passenger intake and drivers ignition is an engine. Vice versa for the other side.
I think you could just tie in another ecu to the rest of the car pretty easy though. If you had ASR this would be really difficult to keep both actuators working right. Throttle linkage is going to be a real pain if the factory v12 stuff does not work. Have fun fitting it in the engine bay.