I feel your pain, but casper's right. The dealer is in business to sell bikes... their bikes. And if they sell you a bike, then great. And sure, they'll sell your bike, only if they make more money from it. Can't really say that I'd trust any dealer enough to sell my bike, or even hold on to it with a dealership full of employees that just see it as "just one more bike" in their way. I can promise you that I'm a little more careful and concerned about my bike than any dealership employee would be. As for marking it higher than what you were asking... it's a dealership.
I wouldn't let a fox guard my henhouse. Unfortunately sometimes, selling a custom or a high-end bike can take time. And I agree, I don't think e-bay is necessarily a good place to sell a bike that commands top-dollar. But, it can help generate interest. I know a lot of people that bought/sold bikes through contacts made on e-bay, weeks after the bike auction ended. Local listings, newspaper, tradin-post, etc are also good places for these types of rides... and word-of-mouth networking. And don't always limit yourself to what an internet site says your ride is worth. Ultimately, it's only worth what buyers are willing to pay.
I hope it all works out, we're anxious to see pics of your new scoot!