One cylinder is not firing....probably not getting fuel. That noise is a combination of normal clearances fromm the bottom end, wrist pin and piston slap. You hear it because you don't have the back pressure of combustion in that cylinder. If you don't run like that too long it will be OK.
Like the pump guy says, the fuel is being blocked in either the injector pump or in one of the injectors. Probably from crud. Both pump and injectors have plungers. Do the test he suggest first. Cross your fingers...if fuel squirts out the pump in equal streams, it is probably an injector. You can swap injectors to find which one it is. That will probably mean buying a cheap injector puller and injector seal washers. Both are very available for that Yanmar engne.
On the other hand, if it is the pump making unequal streams, then I would stop right then and PM the pump guy.
Scotty