Check your disk brake hardware kit...i.e. the brake pad slides, the caliper slide pins, etc. make sure every point of contact is well-greased with hi-temp silicone grease...and make sure every nut and bolt is tight. I had a similar problem with my 2003 and wound up that i had to replace the brake pad slides because they came in contact with my rotor.
Also, Make sure you are installing the anti-rattle springs that sit beneath the caliper. They're called anti-rattle springs or "M" springs, and they're there to help minimize vibrations and so forth.
