hard to tell w/o being there but I've recommended this process and everyone seems to get good or better results:
If your pads are old, get new ones. Take off the rotors and use an electric flat sander with 80-100 grit and get rid of all the glaze on both sides of the rotors (if you know someone that can sandblast them-do it! it's much more even). Motorcycles rotors glaze pretty easy and can be evident. I've sanded my rotors and friends rotors and it USUALLY fixed the problem. If they are warpd, you'll know by spinning the wheel and watching the edge of the rotor.
If you have a loose steering head, the bike will make a clunk or creeking noise up front when you brake. To check that, put your hand over the steering head and upper triple and rock your bike forward with a quick pull of the front brake. You will feel the steering head move back and forth if it's loose.