Front brake issues

[Jbro]

Hey everyone, new to the forum. I bought my wife a 2002 GZ250 that had been sitting for a few years. I finally got the bike to run right a few weeks ago, thanks to all the great info here. I did all the normal stuff, oil, air filter, plug, carb. She loves the bike and has been riding it a lot. She noticed there was a good amount of rubbing/grinding noise coming from the front tire. I checked the pads and they were in pretty bad shape (pieces flaking off). I replaced them and now it seems as if the pads are dragging on the rotor in various spots. Even when just pushing it around in the garage. Is there a way to fix this? Do I need to buy a new rotor? The bike only has about 2k miles on it. Thanks for any help! And thanks to everyone here for all the knowledge over the past few months.