amoller, I don't want to beat a dead horse, but your words have opened up a new can of worms. IF, as Yamaha claims, the dealer never submitted the claim to the mother company and the parts are still there I would claim them as your own. If the dealer refuses and/or has done away with them, it may be time for court action. I would retain legal advise and inform the dealer of your actions. As it has been noted by many, the use of additive are not outlined in the owners manual. I would be willing to bet the dealer never pushes the additives.
This may sound harsh, but it is your money and time we are talking about. The way you presented the case, the dealer had talk with a rep and Yamaha agreed to pay for parts if you paid the labor,correct? But now that Yamaha says no claim was filed the dealer's story is leaking like an old boat.
From your story I read that the CCT/timing chain had been talked about, but no action taken,correct? What happens if the timing chain fails in the next few miles, who will be the warranty authority, dealer or Yamaha.
It sounds like a strong stand and answers need to be presented.
Good Luck