Place your ride on the front stand or place the wheel assembly on your wheel balancer ie (on the axle using two car jacks), spin the wheel and measure or just use a sharpie to tell you the high spots. Your manual will say how much out the disks can be and at what thickness. You can visually see a bad rotor by looking at it. Change out the pads at the same time of the rotor if you do that.


edit: Generally, I have only had to scuff up the existing pads or replace the pads.

 

I am having a similar problem, but after doing the run out gauge my rotors are still within factory limits, though I am probably not too far from needing to replace them. I found some rotors on ebay for ninjas fairly cheap but they are made and shipped from Korea or something like that. Rotors seem to be pretty pricey