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megasquirt will probably control the fuel injection and spark but I need to do a ton more research as to how everything will work



Dude, this will be the least of your problems. I got all the info you need to wire up MS fuel and spark to the 3800. You'll want to tweak the maps for the non-SC motor, but the one's I've got will be a safe starting point. I spent a good amount of time getting mine up and going, but with the info at hand, you could do it in a quarter of the time. GM DIS ignition with the MS is not something more than a couple people have done.

--Dan