Sorry for digging up an old thread.
I managed to address my front brake pulsing issue without replacing the rotors (too much $ for me) and I want to share in a search engine optimized place.
A little bit of history: I agonized over the pulsing front brakes for years. They were lightly pulsing when I bought the bike. Didn't have a workshop so had a independent bmw moto shop look at it. Determined that the front wheel was warped. Found a used one, put it on, new wheel bearing, problem solved for a few hundred miles then came back. This is consistent with reports i've since found.
Lived with it. Learned that settling the chassis with the rear brake helped greatly. This should have been a clue that suspension was part of problem.
Did internet research.
Course of action: 1 replace front brake pads with EBC FA18HH sintered brake pads. The idea being that the harsher pad material will help to in effect machine either deposits or warping from the rotors. Got the idea
HERE. Make sure to thoroughly clean your calipers and ensure that your pistons are not sticking. One of my piston dust seals was not properly seated so after fiddling with it I decided to remove all 4 and clean around pistons with brake cleaner and toothbrush. Use brake lubricant to lube back side of pads and pin. Also, inspect old brake pads to make sure of even wear. 2. Shade tree rotor resurfacing: removed the rotors from the wheels. Marked L/R and bolt registration. Took 120 grit garnet (this is important) sand paper and block sanded the rotors on both sides. Spent about 10 minutes on each side using a good amount of body weight. Also used the block to clean the mounting surfaces. They were very gummed up. Try to be super consistent (flat) here because you are removing material and if the rotors don't match up to the mounting surface -> pads you are in a world of hurt. 3. Mount rotors out of phase from original position. Put the left rotor on the right and the right on the left after insuring that part numbers are the same (mine are). Rotate one 90 degrees forwards on the bolts and the other 90 degrees aft. Torque with new lock nuts. 4. With the wheel off check steering head pre-load. Squatting in front of bike grasp both forks and push fore and aft. Mine had a lot of play. I had checked this earlier with the wheel on and not touching the ground but I failed to sense it. Loosened appropriate bolts and used a cold chisel to move knurled adjustment wheel. That's about it. Put everything back together properly.
Outcome: Immediate improvement. I've since run the bike about 1500 miles and i'm still in good shape. Occasionally, after sitting overnight at least a light pulse will come back. This leads me to believe that the metallurgy hypothesis is correct. The first stop from a speed of a t least 40 mph seems to cure the pulsing. I will also occasionally drag the brakes when safety allows. I'm happy with this outcome.
I hope this helps someone address this problem.