Cobra Brake Problem

Hi everyone, I've had Cobra brakes on my car for ~10k miles now, and since I bought the kit used and was using the existing rotors and pads, they wore out. I just bought OEM Brembo rotors and Hawk HPS pads, and put them on.

When I took my car out to bed the pads, I noticed a disconcerting knocking / clicking sound that varies in frequency with vehicle speed while the brakes are applied. If I brake lightly, there is no sound or anything, but if I increase pedal pressure, the sound will appear and continue to intensify the harder I push.

I ripped the brakes back off and checked the rotors, thinking they might be bad. The run-out was 1-2 thousandths depending on where I checked on the rotor surface. The rest of the system looked fine. The pedal firmness is great, the car stops great, but this knocking seems very wrong. I'm scared to drive the car, but it's the only one I own, so I don't have a choice. I drove it to work this morning, and the problem was still there. Is there anything I may have overlooked? I've been doing tons of searching on this forum, but haven't found anything that sounds like the problem I'm having.

Thanks!

I don't think it's the rotors. That's why I mentioned their run-out. One-thousandth of an inch is approximately .025 millimeters. Spec is .1 millimeters and under.

Update: I bit the bullet, and bought Motorcraft (not OEM Ford) pads at the dealer, and put them on. The problem is gone, so the Hawks are going in the trash. Oh well; live and learn.