I also have a Megasquirt 2 running my NA Zetec on GSXR throttle bodies, there is heaps on info on the web for setting it up to suit your application and the possibilities seem endless if you like mucking around with that sort of thing.
I built it up as a project with my teenage son. (the young ones have better eye sight than me) then wired it into the car. I nearly fell over when it started first kick of the starter.
I couldn't believe how easily it was to get a basic tune with EFI Analytics tuner studio and wide band sensor. that allowed me to comfortably drive the car for a while and sort any teething issues before I get a dyno tune.
You need to enjoy the challenge of a project and follow the instructions carefully and you won't go wrong.