Seeker:
Where are you located? I have a few connections that I might be able to throw your way. The reason I suggest looking at another identicle model is that you will be able to compare. Sometimes, in an essembly line, mistakes are made. Sometimes, it is a bad design. Looking at an identicle model at another dealer will help you know for sure. I would hate to have you pull the trigger on this boat and then find out it was the boat itself with issues and not the specific model!
In the end, use your gut. If you cannot find another dealer close to you, you basically have two options. Deal with the issues as you know them and purchase the boat, or walk away. Sometimes it is hard because they seem like such a great deal. Usually however, you can always find the reasons why. As much as I love Alumacraft boats, if I couldn't look at another one and compare it, and I were in your shoes, I would walk away. The things you described would make it to where you are NOT going to be happy with the end product.
I have OCD "Obsessive Crappie Disorder"