This is a great thread, I love the VFR charging system upgrade.
Megasquirt EFI happens to be something I know a lot about. I have 8 or 9 cars under my belt now. I've seen a lot of back and forth without a lot of clear answers regarding kicking over a MS Bike (a project I have on the back burner myself).
MS EFI allows the programming of a priming pulse. When you turn the key on, it will squirt a pre-determined amount of fuel , adjusted for temperature. IF you are running MS in a Fuel only and keeping a stand-alone ignition I see absolutely no reason why you can't kick it over. In fact, with a port injection I bet it'd be EASIER to start because your fuel should end up sitting on top of the valve ready to go. It won't have to travel through the intake from the carb.
Now, if you plan on controlling ignition with MS too, it adds more difficultly based on HOW you trigger the ECU. If you use a missing tooth wheel, 4-1, 12-1, 24-1, hidden under the points cover, it's going to take at least a couple revolutions to get a sync and even then your RPM threshold may not be attainable with the kicker - you'll have the fuel from the priming pulse but no ignition because you have no sync. The flip side is your ignition timing is going to be more accurate and more tunable!
Now it's also possible (with microsquirt for sure anyway) to use a trigger with the points or a similar two sensors 180 out on the crank with a single "tooth". A Dyna2000 trigger plate comes to mind and would work perfect I bet. The feature is called Dual Spark. The timing will not be as accurate as with the multi-toothed wheel but I kinda think it won't require a sync and should just fire the coil on the first trigger. I'm kinda curious as to whether that works in practice or only in theory. I'll look into it... if it works like I think it works then it should be kickable too.
So bottom line, with fuel only, yes absolutely will be kick-able with some fine tuning. Ignition control... time will tell.