Aside from the advice above....
You have the manual?
http://j30.us/files/yanmar-manual.pdf
You need to be careful with impeller. See the illustration below. You have to set the blades correctly with that pump. If you don't do that, the pump isn't a pump.
After you have checked the impeller, I'd take the hose off the DISCHARGE SIDE OF THE PUMP. Crank the engine, but DON'T START IT. I'd like to know if there is water being pumped out by the pump. If there is, then I'd reconnect the hose to the pump.
I'd then go to the discharge side of the engine water. Disconnect the hose. Crank the engine (but don't start it.) You should see water coming being pumped-out. There are cases where hose collapses INSIDE between the engine and the muffler. You wouldn't see that from the outside because because the hoses are double walled. (THAT's a long-shot).
IF you see water in "force" coming out the back of the engine, then you have narrowed down the problem.