Brakes Squealing

I'm having a problem with my brakes. I got everything back together after my guide pins froze up on my LS1 calipers. Well, I installed a new caliper and this one is working find. Except, when I push on the brake pedal I get a squeal. It's not a constant squeal it's a pulsing one. It squeals at a certain spot every time. I will add that my brakes got really hot when my guide pin decided to freeze up, so could this be a warped rotor or bad pads? The rotor is clean, and there's no sand in contact with it. What do you guys think? Thanks.