Yanmar 3GM30F: intermittent problem with raw water cooling

On a recent holiday our engine overheated due to a collapsed bearing in the water pump. We replaced the water pump and subsequently the pulley but we still had problems with intermittent overheating. We then removed a sweetie paper from the sea water strainer. However, we still have a problem. The engine runs fine for several hours but then when we try to restart there is no engine cooling water coming out of the exhaust. We have been through the entire cooling system checking for blockages but can find nothing. The impeller has been replaced. On several occasions and for no obvious reason the cooling system has started running normally but we have not managed to go for >24 hours without a problem. We are not sure what to do next. Any thoughts?

This is the raw water pump? ..... Yes? it sounds as if you are sucking air in one of the joints. Make sure all have a good seal. Check the intake and shut off area. Check those joints. Also how is the fresh water level holding up, is it retaining its its level?