When you say make the program your own, do you mean map it yourself, or do you actually mean modify the software itself?

IMHO there is no need to do the latter.

I use megaquirt on my corsa which has bike bodies on it and it works great.

Just make sure you get a well built one, there is a lot of cheap crap out there in the world of megasquirt that gives an awesome ecu a bad name.