Update:
From post two weeks ago, Yamaha district rep had told my dealership no such problem exists. My call to Yamaha customer service stated the same thing, then they went ahead and authorized two hours for the tech to diagnose the problem (the district rep had originally told my dealership to do a valve adjustment at my expense even though it's not due yet). Extended warranty did not matter.
7 working days later I called the dealership and they are waiting on the new valves and guides to arrive. So they are fixing the problem. I'm not sure what happened behind the scenes, as the shop has had complete turnover since I bought the bike there (so much for the 6 packs I bought the service techs when I bought the bike) and I have no cozy relationship with anyone there now.
This could go so much smoother with better communication. I presented the Cycle World article, the Aussy service bulletin, and other info, but was blown off as "internet mania" issue by the original service tech when I first brought it in. District Rep wasn't much help either.
Does anyone have a parts list of what they should replace? I specifically asked about the head bolts, and they hadn't ordered those. From what I hear here, they are not reusable. Any other questions I should ask?