Imho, the chances of Yamaha fixing this on their dime under warranty is slim to none. There is no way this should happen to a 1.5 year old bike with 27k miles. You would have to show, and prove to Yamaha that it was a defect in their manufacturing, parts, or materials. The dealer is your advocate in this regard and has to show the Yamaha warranty department that proof. I don't see any proof that their was a defect in manufacturing, parts, or materials though I am no expert. It sounds like your dealer is not advocating on your behalf either? If not, you're screwed.
Something happened. What, is debatable. I still fully believe your dealership lacks competency. It probably never needed to be taken apart. Everyone around here would surely like to know the root cause of why this happened.
No doubt, this whole situation is extremely unfortunate for you.
Why didn't you find a replacement engine? That should have saved you quite a bit of money. And I sure as hell wouldn't trust your dealership to competently rebuild this engine.