you can definitely have megasquirt control the "whole thing" - it's come a long ways in the past couple years.
I'm still a fan of MS1 running the "Extra" code, which is loaded down with a ton of useful options.
The RPM limitations of the old megasquirt aren't really an issue, the version 3.0 (and later) circuit boards all have provisions for high resolution trigger wheels. The limitations for RPM aren't actually "RPM" but, how fast the hardware can "count" the pulses from whatever kind of input trigger that is used. The lowest resolution triggers, which are typically "one pulse per firing event" (distributor pickups, for example, or MSD crank triggers with 4 teeth) are the lowest speed, thus capable of incredibly high RPM... whereas higher count trigger wheels, like a 36-tooth "Ford EDIS" trigger wheel, will record 9 pulses for every firing event.
We run a 36-tooth wheel on an engine that sees 9000 rpm, that is the same as running a standard distributor on a v8 engine to 81,000 RPM. The limiting factor is, a combination of the hall sensor's maximum frequency (teeth counted per second) and there is also a limit in the circuit on the megasquirt itself, which I've never actually tested.
ON a high revving motorcycle engine, a good compromise would be an 8-1 or 12-1 trigger wheel on the crankshaft. YOu'd have no problem tracking RPM to whatever engine speed you need to.
I like high resolution trigger wheels, and running "wasted spark" because it lets you get rid of a distributor, which wastes a lot of energy with it's extra gap (between rotor and spark tower).
I'm always happy to help. Some "high tech" weenies like to poke fun at Megasquirt and it's DIY roots, but I've tuned it on cars and motorcycles that range from Jon Huber's 4-cylinder, 170 cid Mustang that runs an 8.80 quarter mile at 155mph on small tires, stock suspension - to GH's twin turbo big block chevy that holds the AA-BGALT record. It's a rock solid system with many people contributing to development and testing - it's got a ton of features and it's a great way to learn how EFI and engine management works.
-scott