When it is started up out of the water runs fine. Put it in the water starts fine but when you go to accelerate it boggs down and sound like one cylinder is running. It sounds like a fuel starvation issue, is there any common problems with this model?

I assume you are talking about a personal water craft. It is very common for a little bit of moisture in the carburetor to cause this to happen. There is a small fuel needle that is attached to a teeter/totter and is operated by a diaphragm . Often moisture will cause a small amount of corrosion to form on the needle and cause it to bind just enough that you do not get enough fuel when accelerating. If there is enough room in the motor compartment you may be able to take off the cover and clean the effected part of the carburetor with out having to remove the whole assembly. Be sure to lay a clean sheet around the base of the carburetor just in case you drop a part so you do not have to try and find it under the motor plate.