Whatever you do I'd strongly discourage grinding them. Think about this, if you grind the pads, how are you going to get them perfectly flat and level, and unevenness will adversely affect braking possibly to the point of being dangerous. Plus what you'll breath in during the process even if they are asbestos free there's all kinds of heavy metals that are terrible for you to inhale. I've been a mechanic for nearly 25 years and I've never once ground brake pads or machined rotors to make them fit. Remember your safety and the people around you depend on your brakes functioning as they should. Someone else mentioned two different rotor thicknesses, and you say you have the thinker rotors, perhaps that's the issue. If you don't want to talk to the people in the parts store, look it up online at the parts company of your choice.
