3-5 PPMs of bleach in a 50 or whatever gallon res isn't really enough to worry about reacting with any acids enough for toxic levels of gasses to form.
I hope it works out better though. Its sounding more and more like you might have to give in and setup an RO system. Or maybe swap to another nutrient that plays better with hard water sources? I know they make them, but I have no experience with that. Some growers seem to be able to get away with hard water/hydro..
ROs are kind of wasteful, and don't really "filter" out all the water. It just sends the dirtier water passed the membrane and down the drain. Takes roughly 150 gallons just to fill your 50 gallon res, and more or less time to fill depending on the size and amount of stages in the filter.. Gotta do what you gotta do though.
If you were to buy 5 gallons of purified RO drinking water, and mix up a smaller batch in a 5 gallon bucket without it clouding up, I would go ahead and get the filter system. If it still clouds up, maybe your right about the water mold or some pathogens hiding in the pipes, etc..
Seems like without the cloudy res problem you have, you would be very successful!