Scottie,
If you aren't up to "information overload" yet, I'm going to bring up a few more things you might want to research with fuel injection. I only know what I've been reading, and you are probably doing the same thing.
Fuel pump: You're going to need a high pressure fuel pump as fuel injection systems work at about 42 psi with a return line to the fuel tank. With supercharging, you might also need a boost regulated pump if that 42 psi is required to be above MAP. I think these pumps run continuously, so a larger battery may be required as I doubt if you'll be running a charging system.
Fuel injectors: you'll have to determine the "required fuel" for methanol for the horsepower you expect to make in order to size the proper injectors.
Sensors: You apparently can get away with "Alpha N" tuning, as you really don't care if it runs well at anything other than WOT. This means you can probably get away with TPS and RPM sensing. You will probably need a crankshaft position trigger wheel with a Hall or VR sensor to tell the computer exact RPM, unless M.S. can use a tach signal, but there again, most ignition systems use wasted spark. The Megamanual and Megasquirt forums should be able to answer those questions, but there are not a lot of examples out there with Megasquirt, EFI, and supercharged vintage pushrod motors.
Other sensors you may need are MAP, AFR(wide band) and EGO or CHT. I don't think you will need CLT or IAT as Megasquirt can be set to ignore these numbers. In fact, M.S. does not even use A/FR after 70% throttle opening. But, a good A/FR gauge is the first best gauge you'll ever want after a tachometer, as it will get you close on jetting even before a dyno or salt flat run. CHT or EGT and oil pressure are nice to know, but you just can't look at them at 150+ mph! A data logging system is essential for reviewing data between runs. I've gotten away without one so far (just lucky, I guess). I believe M.S. allows data logging that you can review after your run without having a separate data logger.
The only gauge I can monitor while riding is my big Scitsu analogue tachometer, and I keep my clutch hand at the ready for anything that might go bang. With the data logging system that I have installed for this year, I hope to learn a lot more than what my seat-of-the-pants system has taught me.