Actually, only one ECM should control the IAC. ECM gets no feedback about IAC position. It only knows what it has commanded for counts. A sticking or unresponsive IAC or in this case, and ecm sending opposite commands, will cause the IAC to move out of synchronization with the ECM's expected position.
I do not believe I would use only one 5V line. However, the resistance type sensors are part of a resistor network with a terminating resistor in the ecm. Adding a second terminating resistor can alter the total current through the sensor and therefor the voltage reading at the ecm. There are a few people that have published the results of trying to use dual pcm's. I can remember one individual using a 7749 for engine control and a 7427 for trans control in a Syclone and I seem to remember some sensor had to be duplicated. I'll have to see if I can find the information he posted.
The stock dual plane manifold is divided left and right bank. Each side should have it's own injector. I would expect no trouble with individual bank fuel trim. What would be interesting to me is, after enough time tuning, if VE and/or spark tables end up slightly different between L and R banks.