Probably not worth the hassle. The fairings will not match up from the '06-'10 r6's going onto your '03-'05/'06-'09 r6s. Hell the fairings off a '08-'10 will not match up on the '06-'07 without redrilling and messing around. I have heard of people redoing the tail only, but even then you will need a new subframe and a bunch of time modifying it to fit your model.
Good luck if you attempt to get it done, you're gonna need it. If you change up the way your bike looks, I'd recommend getting the shorty can for your bike.