Depends on the denatured alcohol being used. 90% Isopropyl alcohol is preferred over 70%, if you can choose. Sounds like the rotors were not as clean as they should have been and the pads got contaminated. Clean the pads with the alcohol. Once dry, then sand them, as mentioned above, with fine grit on a flat surface. Then re-bed the pads to the rotors and this SHOULD resolve the issue. 10 hard brake applications per brake from speed - but not to a full stop. This should get them performing as intended.
Otherwise, caliper alignment MIGHT be the issue. But probably not. But make sure they're tight. I'd make sure the rotor is torqued properly to the hub. And then check the hub for bearing play. Check the replaceable derailleur hanger/dropout also to be sure it's tight, square and plumb. And issue there could cause the brakes to create a vibration that would transmit through the bike - and saddles!