Actually, the megasquirt replaces the stock ECU. However, I do not know if the megasquirt has enough "horsepower" to run COP ignition and sequential fire injection. I just have not looked at it lately.
I can also tell you that if you dont understand the factory wiring, you will not be able to do the megasquirt. If you dont want to get on the steep learning curve required it might be in your best interest to have a rod shop do the wiring and tuning on the engine. It might not cost you any more to pay a knowledgable EFI tech than it would to buy, build and attemp to tune an aftermarket ECU.