MSefi.com read only forum (Jan.15,2018)

I don't know about the Honda magneto, but the wire you use to ground/kill the magneto on a Briggs/Tecumseh definitely has a signal in older engines.

Well, I was thinking that signal pickup might be the problem.
A standard ignition system coil needs a ground to work.
A magneto ignition system ...

Some specific questions:
Can I use megatune to control the throttle?
Can I use MS-II with a pull start engine?
When I have the gauges up on the screen (RPM, MAP, throttle) the RPM is red. The engine has a magneto on it and it is connected to the MS-II. Does this mean that there is something wrong ...

The "easy" fix is that parts (ECU's Injectors, Sensors, etc) are all available for that engine on eBay for reasonable prices.
Diagnose the part(s) you need, buy the part, install it on the car, drive the car.

The MS option means that you will be designing and implementing your own EFI system.
You ...

Personally, I would stick with a carb and investigate adding a simple choke.
I'm also not sure WHERE you'd mount the megasquirt controller (since it'd be either in the hot engine area OR in the boat and subject to water).

Also, you REALLY want reliability on a boat so adding complexity might not ...