Wendel,
It is a great time of year to sell a boat. I would fix it up the best that you can, putty up the cracks and paint the entire area. You should also replace the prop and lower unit casing for appearance sake. I would not hang onto that boat, it is an accident waiting for a place to happen.
A few comments:
The boat is 9 years old so you should not expect a manufacturer to honour any type if warranty. Put yourself in their shoes, how do they know what the boat has been subject to and exposed to?
Based on the photo showing the skeg, I would say that you hit something at a good clip. This may have caused the cracks. If the boat sat all winter and hot and cold, the expansion and contraction would cause the cracks expand. These cracks are minor because the area is just the splashwell for the transom.
If the transom has a significant bow to it the wood under the aluminum is probably rotting and needs to be replaced. This is a huge undertaking that requires professional knowledge. I would not attempt to do this on your own.