No you don't need a Power Commander. There is a little program called Tune Ecu available now that allows you to change the maps on an EFI bike at home with a laptop using a $20.00 Vag-Com cable that you can order from several places.

If you only remove the end plate and the first baffle you won't need to mess with it.

EFI=TuneEcu
Carbs=Jets