How to Megasquirt your 3G Hemi

I'm not aware of anyone doing this. Are you? I 'm not sure I can agree with you that the second plug is 'not needed' - mopar wouldn't put it there otherwise.

Anyone know the main reason or list of reasons mopar put two plugs?

I believe the main reasoning behind the two plug setup was the original wasted spark design of the engine to help clean up the Hemi's somewhat notorious emisisons issues. The engines breathe so easy that they can pull intake charges straight through and out the exhaust port. The early engines had all the wires across the engine as you might recall, so one coil pack fired a plug in its respective cylinder and the one opposite it in regard to firing order. They weren't necessary designed to fire at the same time, though I see no reason they couldn't do this. Would potentially offer a more consistent flame front, but at the same time it can cause two wave fronts to collide which can be a big detonation problem.