Were you able to get the water pump to pump? I believe my problem is similar so I'm eager to hear more about your progress. I removed the screw at the top of the power head where I might install a tell-tale but no water pumps (I backed it into the lake just to test) and I ran it about 30 - 45 seconds. As far as I can tell, the impeller and water pump housing aren't bad enough that something shouldn't pump. I can force water up the brass tube with a hose & get it to come out of the screw hole so I don't suspect any blockage.
A local boat mechanic suggested that I might have a blown head gasket or exhaust gasket causing water to escape before getting to the top of the power head. The engine seems to run just fine and I didn't detect any steam or air pulses from the screw hole at the top so I'm not sure if gaskets are my problem.
Have you considered the possibility of blown head gaskets or exhaust port gaskets? I don't want to pull the head or exhaust just to check but that may be my next option unless you found something in your quest. Again, I'm eager to hear your results!