Something is very wrong! Possible causes are failure to retract the caliper piston fully, using a C-clamp or similar tool, pads that are the wrong dimension, pads not properly placed or seated on or in the caliper piston, the wrong pads for the application, failure of the caliper to slide properly on the pins or bosses, failure of the rotor to seat in the proper position, foreign objects, etc. My guess is defective or wrong application pads. The shop manual doesn't list the original thickness of the pad material, just the minimum, and it does not list the backing plate thickness. Your gonna have to compare with the old parts and guess a bit.
BTW, myth or factual, rotors do develop excessive runout...whether due to warpage or other factors. That is why there is usually a "maximum warpage" spec in the manual. No matter what the cause, it is important to check runout as well as rotor thickness when doing a brake job. Rotors can and do fail the runout spec. Also, I would not expect to see a warped ventilated, thick rotor for a car, but I have seen the thin ones for bikes and race cars fail a straightedge test when removed. If that is not warpage, I don't know what to call it.
If you end up in a box, give a call and we can study it and cuss at it together.
