Assuming your timing is correct, compression is good and all megasquirt wiring and settings are correct then you only have two things you should mess with to get the engine to fire: Required fuel setting and idle screw. I always turn the idle screw so that the butterfly in the throttle body is opened pretty much all that the adjustment will allow for the first firing of a new megasquirt install, that way the engine gets plenty of air. Yeah, idle will be real fast, but then it can be adjusted down once the engine is running. Then changed required fuel up or down depending on wet or dry spark plugs. A common problem is too much fuel on a new install and the spark plugs getted fouled, then it is hard to start even with the correct settings. If you suspect this try a new set of plugs. If you think you flooded the engine, then you can push the throttle all the way down while cranking. This automatically puts megasquirt into flood clear mode so it does not inject any more fuel allowing you to start a flooded engine (just like all modern EFI systems).
From my experience, every engine I have ever started fired right off with the required fuel calulated in megatune. I have never had to change the value just to get the engine to start. I have needed to open the butterfly to start several of engines because they had a cold air idle motor that ended up being removed by me during the install so they all suffered from not getting enough air through the throttle body and would not idle correctly.