There are a number of guys running the ebay wavy rotors (including myself) with good results. I think the "bang for your buck" factor is larger if you have one of the earlier bikes with the smaller disks and the single pot calipers (don't remember the year they changed). This will require you to get caliper adapter plates from either Sean or Jedi.
ON the rear, I didn't see any real performance increase, the stock rear seems powerful enough.
This is the 3rd year I've had my wavy rotors and I've not had any trouble only great braking! I will be upgrading to the Busa calipers w/ Sean's adapters either this weekend or next since the bolts I ordered finally came in. Now I will have a even better set of stoppers on the front.