I don't think you need to do an acid flush on anything but the heat exchanger on a fresh water cooled engine. The only place that you will get salt and organic buildup is in the heat exchanger. I've never done this on my engine before as I just recently converted to fresh water cooling.
No, you do not need to acid flush a fresh water cooled engine. You may need to clean otu the raw water side of the heat exchanger... a simple vinegar rinse out should do just fine. I would run a hose thought the raw water side and see what flow you have..if it seems fine then leave it alone, if it seems to be a bit slow flowing through then vinegar should clean it out. Since the ehat exchanger does not get as hot as an engine there is less likely that you will have a build up.
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