Well I think we can close this post. Got my bike back (again) yesterday, repaired a slight oil leak on oil cooler assembly, changed both rear running light sockets (kept blowing bulbs) and had the front brakes looked at again.
Service manager drove the bike, working the brakes to warm up the rotors, engaged ABS and all to be in working order with no abnormal noise, fork movement or pulsation.
L/H has .001 run out
R/H has .002 run out
I am told these values fall within Harley specs.
I drove the bike and the front brakes felt different, with no pulsation as previously experienced. I asked David if they had cleaned or done anything to the brakes, he replied no, only that he had worked them hard.
I am a loss, while i'm pleased the brakes no longer pulse, I still want to know why they were doing it before. Uneven pad wear? Glazing of the pads? Dirt debris? Beats me..I keep the bike clean, maybe I'm not whomping down on them hard enough.
Thanks for everyone's feedback and suggestions around my problem.
Before I left the dealership I ordered the Harley service and parts books for my bike. Information is a good thing. Should have done this when I bought the bike.