Update
The shake has come back as of my ride home from Oregon on Thursday. I spent 4 hours at the dealership where I bought my bike on Friday. The service manager called Yamaha and didn't get the answers that he was looking for. The "factory" Yamaha Tech in California gave the service manager new suspension settings. I told the service manager, I have already tried several suspension settings but we can give the "yamaha factory techs" settings a try. The service manager rode the bike before and after the settings. When he got back from riding the bike after the new settings were installed he said, " It seems worse to me now than where you had it set." Thanks "haulinash". LOL After that, I spent about an hour on the phone with Yamaha customer service. Basically they said, " the service manager needs to talk to a different tech and get some other ideas on what to check." Today I went over to a friend that I ride with house where we have a static tire balancer, the type they say to use in the owners manual. Since the weights to balance the tire were next to the valve stem, we decided to spin the tire 180 degrees on the rim and rebalance. We did and it only took 1/2 the weight to balance this time but the weight was still needed in the same place. Rode the bike back home and it is now worse than when we started. My hands were numb from vibration and the head shake is worse now than ever. So now I am banging my head against the wall as we speak. I am truly disappointed with Yamaha. I was there on Friday (for 4 hours), and yes I had an appointment. NOTHING was done to the bike except some suspension settings changed.
I am thinking that I just have a bad tire, plain and simple. I ask the Yamaha customer service rep about the possibility about replacing the tire and he told me that was probably not the problem. I am going to order up a set of PR3's Monday morning and install them next weekend. I sure do hope that fixes my problem.