Hmm.. Well good to hear that you got it sorted, but i'm a little worried about what you just explained.
From the outside to inside, the order goes caliper/piston, shim plate, brake pad, rotor (disc). Theoretically if they're installed properly then the shim plate and the rotor shouldnt come close to touching because there is a chunky pad between them. Anyway, you've got the issue sorted so I guess thats all that matters!