You just toss the stock magnum computer and run the engine with all it's original parts if you would like on the Megasquirt. It's real easy to change a sensor, injectors, etc later if you upgrade. A couple of menus and you're done. You will have to add a pull-up resistor to get the cam sensor in the distributor body to work but that's not a big deal. My LA 340 has all GM sensors, a holley throttle body, the stock magnum distributor for a cam sensor, and a 36-1 wheel on the crank. I have sequential multiport injection with coil near plug coils from an LS based truck engine. Car started and idled the first time I ever cranked it and it has autotune. I have an MS3 Pro.
