usually a jacked up rear is a good thing for handling, and with out lowering links i doubt you'd be able to lower it enough to even notice, i dont know about the R1 but usually the ride height adjustment is just good for a few millimeters, not inches

those pipes look so good with the stubby tips, looking awesome but yea definetly do something with that fender, and i'd check out a targa seat cowl for it too if you haven't already