99 WR400 with new Warp9 Rims

Hey guys, I just put on my new warp9 rims and I am having some problems. The first rotor I was sent, was apparently warped (thats what the guys over at yamaha said after they dial indicated it). Warp9 is great, they mailed me a new one right away. Still however I had the problem of the rotor being slightly too large in diameter. Only on part of the rotor would it rub the inside of the caliper. Being fed up, I ground down the nubs on the outside of the rotor... that dont even come into contact with the brake pads, not sure what they are even for, to make the rotor look cool?

Well after that I no longer had the problem of the rotor hitting the caliper, but now when I am going more than 10mph and use the front brakes I get a nasty sound. They still work, it just sounds like something is scraping. Not necessarily metal on metal. I am not too familiar with the details of how brake pads work with rotors that have so many cutouts in them. Is it possible that the brake pads need to somehow adjust to these more machined rotors than the standard rotors that the bike comes with that are only drilled?? That sounds ridiculous to me, but I really don't know why it is making such a loud scraping noise.

Any ideas of suggestions would be great. Maybe someone has had a similar experience when switching to aftermarket rotors??

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