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In preparing to rebuild the water pump, I have removed the water pump housing, impeller, Outer plate that sits under the impeller and the gasket, right down to the oil seal housing. There were a lot of white crystals nearly clogging the water channel of the oil seal housing. I can not tell if there is more debris further down the channel.
I would like to know should I submerge the entire lower end ( only the propeller off and the water pump removed ) in a pail of Vinegar over night to try and clean the calcium deposits that may be in side the lower end casting cooling water channels.
Or is there a better way to achieve this.

Any suggestions appreciated

I would use drill bits, hangar wire, etc. to physically remove what you can then pour vinager through for short soaks. I wouldn't soak overnight though.

One of the local outboard motor repair guys - who is very well respected - uses "The Works" toilet bowl cleaner to open up the water passages. It obviously won't dissolve salt, but it dissolved the calcium and the shell bits, etc. The salt crystals are usually stuck to those, and come out when they are dissolved. My starboard motor had some plugging due to being run aground, and sucking up shell pieces. He recommended removing the thermostat cover and thermostat, squirting The Works in there, and then quickly putting the cover back on, start the engine, and run. I did it a bit different, by shoving a foot-long section of clear hose in the thermostat hole after squirting The Works, so that the dissolved "stuff" went overboard. And you could see the stuff going over the side. Obviously you don't want to run long - just maybe 5-10 seconds. First time I did it, it resembled one of those volcano projects you made as a kid. The foam-back after squirting in the acid was considerable. Second time yields much less. Yep, the label indicates this is a mild acid, so be sure to hose off the runoff on the outside of the engine. It made a noticable difference in the engine cooling.

I would second what the other Tom said. I've seen bad things happen to parts left too long in vinegar. We went through 5 gallons of vinegar last year doing a thorough de-clogging of the cooling passages in both engines.

For what it's worth, a hand squeeze fuel pump ball helped get some pressure behind the flow. Good luck.

Tom
Dream Catcher - 36041
http://www.tendervittles.net