Scrapper

Are you breaking them in correctly (no pun intended). Most pads and rotors have a specific break-in procedure to burnish them. Also, did you rebuild the parts yourself or did you purchase them as remanufactured? Either way the quality can really suffer, it's sometimes worth it just to get new replacement parts. (Especially when it comes to master cylinders, if the bore is even slightly overlarge the seals wont do their job and you'll get nothing but sponge). Finally, how did you bleed your master cylinder and calipers? Most master cylinder's have a bench-bleed procedure (prior to mounting on the bike). Also, you have to make sure that the bleeder screw is at the highest point of the caliper when bleeding a dry system, or you'll get air trapped in the interior of the caliper. Even with all those precautions, bleeding can be extremely tedious and need to be repeated occasionally for weeks before you'll get all the air out. Good luck getting it sorted out!

PS - if your pads are glazed they're essentially junk. Glazing comes about when you've overheated the pad (generally from not following proper break-in procedures) and the "glue" that holds the friction material together actually boils to the surface of the pad.