Thats not quite correct - there are a few different types of engine position sensors that can be used, and different types of ignition coil.The box isn't in any way "engine specific". It's the fuel and/or ignition map - which you program into it with the megasquirt software and a laptop - that's engine specific.
Right now the box is going to be configured to work with a crank sensor. You could setup a crank sensor on the 900, or you could get the megasquirt changed to work with the hall sensor on the 900. Possibly best to leave it as is, and fit a crank trigger wheel to the 900, because ultimately you'll end up with a better ignition system. The forums at www.msextra.com are a great resource of information.