The M3W is locked into the Harley '06 and earlier Twin-Cam motor primary cover bolt pattern. The new Harleys, '07 on, have a five bolt pattern and the '06 earlier have a four bolt pattern.
Moto Guzzi motors at not as large as the S&S. They may have more HP, but their torque will not be as high as the S&S motor.
If you're looking for more power, the only way would be to do a big bore kit on the S&S along with cam and different TB with larger injectors.
Now if you wanted to convert to an "F" series and replace the S&S with the original Miata motor, I believe you could get tons more power, but the revs would be very high compared to the current setup from MMC.
IF you wanted more power, you really need to be thinking about the rear wheel. I believe the Polaris Slingshot has a 10"+ wide wheel in the rear and they break loose often as well.
Either way, the S&S is still the best way to go.