92 Loyale brake noise (clunking)

I recently replaced the rotors on my Loyale, the pads had about 80% life left so I put them back on (maybe a mistake?) It was fine for a day or two and began to make a clunking sound on the right side when coming to a stop and eventually turned into a constant clunk, clunk, clunk all the time. The clunk does go away when the brakes are applied firmly, if I just lightly tap the brake I can feel the clunking through the brake pedal. I installed new anti-rattle clips and made sure the axle nut is torqued down. So, here is the crazy part I can't figure out. If I remove the brake caliper and the pads and just put them right back on the without changing a thing the clunk goes away completely for a day or two and eventually comes back. I just took it apart for the third time and put it back to together and the clunk is gone but it won't last long. I had a brake shop look at it and they couldn't find anything wrong with it. I'm at the end of my rope. May try new pads and see if that makes a difference. Thanks the help.