I have the same engine in my '78 C&C. This spring I had to rebuild my waterpump because a replacement was too expensive. Yanmar wanted about $600 to replace it. But I bought replacement parts for about $80 and totally rebuilt the pump. As long as the housing itself is good it is a pretty simple job. You can get an exploded view of the engine here: literature
(thanks to NOLASAILING)
In spite of the rebuild though I have had similar problems with air getting into the water intake pipe and breaking the suction after or while I was being bounced around by the waves. I don't think it is because the water intake was too close to the surface, but I don't know definitively what caused the problem.
You said the Housing and cover plate were worn. Try a new cover plate and a new gasket. Or if the outside of the cover is clean and flat, turn it inside out. You may be loosing suction here especially since you said you have a leak.