Okay, if you'll be utilizing the 420A input modifications, then you'll need to let Megasquirt know what signal to expect. Per your MSQ, it's currently expecting that simple 50%DC pulse I mentioned. It's actually getting a much more complex signal from the crankshaft angle sensor.
Under "Basic Settings" and then "Codebase and output function" you'll need to change "Neon/420A decoder" from "Off*^" to "Neon/420A."