Here is my experience. First I put new brake pads in, it got worse, I mean rally bad. Next I took the calipers apart to clean them and reassembled. (I checked the rotors with a dial indicator and found no noticeable run-out, so eliminated this as a cause). When I was bleeding the brakes with my vacuum bleeder I noticed some gummy dark brown chunks coming through the bleeder line with the brake fluid. I took the bike out for a test drive and the brakes were fine, no more pulsing and very smooth at any speed!
My theory is that there was a build up of gummy brake fluid / crud? in the channel inside the caliper. One piston was working and the other was plugged, causing unequal pressure on one side of the rotor when braking and resulting in the pulsing effect.
I am going to take the calipers apart again to see if I can clean the channels to verify my theory, (although I think all the crud is now cleared).