The bike is back home and have about 300 miles on it since the work was done.
The rear head gasket was blown and needed to be replaced. They clearanced the rocker boxes the front was almost done as it had worn a large gap into the rockerbox all on its own. When they were in there they found that the rings needed to be replaced and the rear cylinder needed a ball honing some small scratches in the cylinder, nothing you would get your nail caught on but enough you could see the trend. I went and bought new rings since the dealer didn't have them I had to drive 2 hours each way to get a set to get the bike back on the road for the weekend.
They also found a broken flange on the rineharts, at first they made mention of this to me then realized they were the only ones to touch the bike and said we replaced it cause it was broke. Good enough it was taken care of.
Have had to retune the front cylinder a bit due to the pressure change and it not leaking. Just glad its back together and running well.
Still waiting on the paint to be replaced though, but the dealer is working on it.