A 12JG pump is good, there are better pumps but you only need to go that route when making serious power. The A stands for the cut impeller that was originally in the pump. A is an aggressive cut and unless your making some good power your not going to be able to spin it very fast. In a stock application you would probably spin that impeller around 4000-4500 RPM. I'm spinning an aggressor A+ impeller 5400 RPM in my boat and i'm pushing close to 700 HP. You can have the impeller cut to match your application, there are advantages and disadvantages when doing that.
A high rise intake manifold will probably help make a little more power, but i don't think it's going to be noticeable.
Do you have any pictures of the boat? What are your goals with this boat?