After reading my own thread the GSXR throttle bodies are actually 46mm. The opening is 48mm, but it necks down quite a bit. so it's the number that sticks out in my mind. My Jenvey ITBs are 48mm straight through though.
A 45mm throttle body is probably large enough for most things. If you know what you're doing (I don't necessarily) tuning the intake for a specific RPM range or output, there's probably a formula out there for optimum size. I just know from reading that with EFI, having a large throttle body won't hurt performance (nor will it necessarily gain any). I'm sure someone far more knowledgeable than me will come along.
Anyway, you seem to have everything else worked out in regards to Megasquirt. Good luck, it's a steep learning curve, but with MS3x, they've made it quite a bit easier.