There is no need to relocate this pump below the water line, in fact I would suggest against it. It is self priming. We have several Max 3 & 4 pumps on the boat and the diaphragms can be fouled by the tiniest grain of dirt or sand. The triple diaphragm system is so complicated that the repair kit includes the whole triple diaphragm unit already assembled and ready to install. I'd replace the triple diaphragm and see if that helps; it won't hurt to have a spare onboard anyway.
Otherwise, about the only other way these pumps will fail is if you are getting air in the line before the pump. If you can't locate an air leak, pressurize the intake line (close the seacock) using this or another pump. Also, you could attach a hose from ashore to the intake while running the pump and try to blow the lines and diaphragms clean, but this could damage the diaphragms. In theory, this pump can run dry so you don't have to worry when messing about that you will damage anything by not having water running through it.