I had another problem many years ago that showed the same symptoms. The two bolts that carry the caliper had seized up where they should have free play through the caliper. As the caliper could not travel perpendicular to the disc, any discrepancy the disc had while rotating was telegraphed through the pads, pistons, right up to the lever. I won't disclose exactly which bike of mine it was as it would be a little embarassing. May be worth a check ?
Good luck.