What did you use to clean the rotor and how did you go about bedding-in the new the pads, i.e., did you just ride the bike and use the brakes or did you cycle the brakes per Avid's Pad break-in instructions?

It typically takes about 20 - 30 successive moderate to hard stops from 12 - 20 mph to bed-in the pads to the rotors and re-burnish the brake pad surfaces such that full brake force is achieved while brake squeal subsides. Then again, if the rotor were really cooked it could take some deep cleaning with brake cleaner to get them shaped back up to where they can be re-seasoned, or they may be toast even though they don't look that bad.

Keep us posted.