Originally Posted by Kyle@STILLEN

The surface of the pad literally cooks into the rotor. I may have pictures of this as I have seen rotors come back from customers with the imprint of the pad on the friction surface of the rotor. This transfer of material creates a rise in that area of the rotor. Once you've done this, you will experience a pulsation from here on out...you need to cut the rotor and get back to fresh material. With that being said, just because you can't see the pad outline in the rotor doesn't mean you haven't created an uneven pad transfer area in the rotor friction surface.

Another problem may be your the material of your Project Mu pads. Sometimes using two unlike pad compounds can create a mis-match on the friction surface. If you did not clean up or re-surface the rotor before installing your new pads, the different compounds from the old to the new pad may not be playing nicely together and are not allowing a fresh transfer layer to be applied. The only way to resolve this issue is by cleaning the pad surface either on a brake lathe, or with some cleaner pads...Someone mentioned earlier using a special type of sand paper, this is basically an abbrasion material designed to scuff up the surface of the rotor to remove the old pad material from your friction surface.