Kev .... if the engine was submerged and there was water in the piston bores then you will need to do a lot more than that. All the filters need replacing and the oil will also need changing. Oil and water don't mix and what you are probably hearing are the tappets not being lubricated probably because of the oil/water mixture. You might in fact block the oilways with this "sludge" and damage the engine. I would buy a good flushing agent and then change the oil. Hopefully you wont have damaged the engine already.
Chris, July 2007