What ignition switch are you using?
If you are using the stock switch, there is a brown wire that goes hot during cranking but is cold during run. There is also a blue wire that should be hot during run and cold during crank. You could tie these together, but my understanding of the new Hemi's is that when the switch goes from start to run there is point where both wires are cold and the PCM doesn't like it. But you have Megasquirt so no idea if they have the same issue.
One option would be to add a push button start. Then everything is hot at all times but the starter can be engaged only when the button is pushed.