Its not something what i would like. Making some "hybrids" like that is not a good idea. EMU does not know to control Auto gearbox at this time, but it can send revs, speed and other informations to outputs.
Basicly, the first two problems i see are this:
You need to keep OEM ecu to work without trouble code, so everything should work for this ecu. For example if you control injector using EMU, you need to put resistors to OEM ecu injector outputs.
Second: If you use one sensor for multiple ecus, you can affect values with additional input resistence, or if some sensor uses pull-up resistor to 5Volt (like most termistors do), you need to disable it on one ecu, and the idea must be the same on booth ecus- So sometimes you need to double the sensors, and give one for each ecu.
So i see many reasons why not to do this.
Do you know the Ecumasted DET3 unit ? Its very smart piggy back and it can basicly just adapt your ecu to work with bigger injector, change IGN timimng, or you can remove MAf using that. Its also much cheaper.