This is what you need if your caliper pistons are dirty Service / Tech | Lyndall Brakes

 

As I said in original post already cleaned caliper pistons and greased anti rattle spring

 

I ran into this last year after having new tires put on. One of the rotors got slightly bent during the change. As the tire rotates, the bent rotor forces the pads out. The first pull of the brake is soft as the pads are getting pushed back into place. A quick pump and you have firm brakes. Then the cycle starts again...

 

If they were working fine before and you didn't open the system then I would check the rotor alignment. That was what you removed, most likely the culprit. No offense but some diagnostic suggestions don't really make sense here.