brake pads won't fit

Pistons aren't all the way back. Could be crud behind the pistons, as Del suggested. If that's the case it's time for a caliper rebuild. I wouldn't do anything to the pads, if they're the right part the fact that they don't fit suggests something else is wrong.

I've never had a set of disk brake pads not fit if they were the correct pads for the application, regardless of new rotors etc. So either you've got the wrong pads, or something else is going on unless you can prove otherwise.

A company making the rotors or the pads too thick isn't usually an issue, usually it's the opposite to save money on production. What brand are the pads and rotors?