Doug, try this:
First thing, was your wheel trued up? You could have some wobble.
Also, how even is the wear on the rotor? You could have a high spot.
Loosen the Brake Spring as much as you can w/o removing the screw.
Press in on the caliper towards the rotor from the left side of your bike to fully push the piston all the way in (well, as far as you can get it).
Readjust the the caliper spring (I remember that you tighten it until the inside pad touches the rotor, then you back it off a 1/4 turn).
Spin the wheel, no squeak?
If no squeak, spin the wheel and stop it with the brake. Spin it again, Squeak?
If so, the your piston is not retracting. Could be a couple things.
First easy thing, poke a guitar string through the second small hole in the master cylinder, could be a blockage (with the pressure, gunk could have moved up and down and become lodged in the small hole).
Did you replace/check the caliper upon your rebuild? (remove the piston, check for pitting, replace the rubber seal, clean the groove the seal sits in, etc.)?
If not, it could be the rubber seal. Remove the caliper, and remove the piston from the caliper. Also, remove the seal. Fit the piston back into the caliper, should slide in easilly when it is straight. If it does, thoroughly clean the seal groove and replace the seal.
I did the brake dance on my 550 when I originally got it. I did all of this to some degree, hope it helps.