cleaning scale on the inside of the water jackets

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I have a 2 cycle seadoo. I have the head off right now as part of my winterizing. I have a white scale build up on the inside of the water jackets that surround the cylinders. I was thinking of using CLR (calcium, lime, rust) cleaner to clean the build up before added the antifreeze. CLR's web site does not recommend using CLR on aluminum since it will remove the finish on aluminum. I figure the scale build up is from the calcium and or lime that is in the fresh water that I operate in. Does anyone have a recommendation for a water system cleaner that is save to use on a Seadoo aluminum engine?

UPDATE 11/19/201
As part of my winterizing on my 2 cycle SeaDoo GS. I remove the head and the top part of the water jacket. I pour anti-freeze directly into the water jackets and it normally it runs down the cooling system and into the engine cooling system drain hose. Which will then drain out of the exhaust pipe. In order to make sure that the anti-freeze mixes with any pockets of fresh seawater that are still in the engine, I pinch off the engine cooling system drain hose (this is mentioned in the shop manual) so the anti-freeze will back up and fill the entire cooling system.

My concern is that the drain hose does not have red anti-freeze in it, and it should. When I stopped using the ski a couple of months ago, I was getting a flow through the Cooling System Indicator near the stern eyelet which indicates that there is water flow In the cooling system.

Is this an indication that there is blockage between the exhaust manifold and the drain hose. If so, is there a way to address this? The drain hose connection to manifold is not easy to get to.

Any advice or has this happen to you.
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Hi Lakedude & welcome to the forum.

I know the people who run in Salt water recommended "SaltAway".
IDK if this would work on just regular scale build up.

What city are you near?
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