I dont know much about this swap but I do know to make the cr run it doesnt take much, just a couple wires and it will fire up. Just meake sure you find a complete engine with all accessories on it to make your life easier. Hook up main power, ground and switch power to the ecm and it will start. You will need to hook up the obd2 wich is 3 wires on a 05 and earlier and 2 wires on a 06 and later and a recovery file from Smarty.
To run an auto you will need the PCM with it as well and all of the harnesses.
I am not sure how you make your dash gauges work, its probably not difficult but I have never done that swap so I am not sure. You could proabably run the gas ecm as a piggy back and just use the couple senors out of it for the dash gauges.