Ben, having spoken with three different brake pad vendors, there was ONE common comment from them = the discs have to be CLEAN (NO brake pad transfer material) in order to bed in the new pads with the exception of metallic pads like the Hawk Plus, as they will dig through to a fresh surface (i.e. scrape metal off !!). When I put the HPS pads back on the front after killing the OEM pads they simply would not even START to bed in until the disks were turned. Swapping just the pads could present some real problems. They RIGHT way to do it would be pads AND disks, with all parts marked for their corresponding corners.
When I spoke with Cobalt they insisted that since their pads actually deposit material on the discs, the pads are working against a surface that is coated with its own material so it is like pad material against pad material, and thus no wear on the disks. I spoke with some local road racers who confirm the insignificant disk wear when using Cobalt pads. Cobalt said they will work well when cool, yet tolerate temps up to 1600 deg F. They are about $200 per set, and I have the part numbers if needed. The part number is for the backing plate for the pads and then you select the friction material, and thus some of the f/r brake bias can be "tuned".
Kenny, about the only effective way to measure the warp (runout) is with a dial indicator on a brake lathe. There is a method to do it "on car" but it's a hassle and the dial indicator kit can run $100 plus. Since the degree of warpage is in thousandths, using a flat edge is not going to work. Again, swapping stock and HPS pads will NOT work.