The two bolts that attach the rear caliper to the frame are two different lengths. I've read that installing them improperly (reversing them) can cause brake problems. Could one of these problems be making the rear pads drag?
Not sure if this would cause what you are describing.
Since your bike is a 1999 vintage, and if you have not yet replaced the rear brake line, this is most likely the issue with a drag you are experiencing.
Old lines get crud in them and eventually won't let the pistons retract.
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