What is the cost of freshwater in your area? Diluting your seawater will lower salinity as well as your high magnesium and calcium levels. It will also dilute "bad stuff", but as long as you are sticking to organisms that live under the same conditions as the water you are collecting, then there is no reason to alter it.
Sediment filtration, carbon, and ozone will help with clarity. The refugium will polish the water and harbour live food (plankton) for the tank inhabitants.
Your lack of water movement will greatly diminish water quality, but that will be rectified once you get your prop pumps going. I would consider adding peroxide once you get the pumps going to increase redox potential, oxidize excess organics, and improve water quality/clarity.
Macroalgae in the display tank will also increase the dissolved oxygen level and remove Co2. It will outcompete nuisance algae and reduce nitrogen and phosphate levels. I'm sure you can find lots of tangs or parrotfish to eat the algae once it has done its job.
What kind of sea life do you have immediately behind your property? Usually bays/harbours are shallow with a lot of evaporation so the salinity (and calcium, magnesium etc.) is higher than neighbouring reefs. Habitats along the shore are nutrient dumping grounds as living and dead organic matter washes in from the sea. Some areas get a lot of dead algae that pollute the water, further lowering dissolved oxygen levels of calm water, while other areas get highly oxygenated water from wave action and currents. The sps dominated reef I visited in the Red Sea started within a few meters of the shore with clearly immaculate water quality and clarity. At the other end of the spectrum, I've visited a few Florida marine fish collectors that have oceanfront property but have to use salt mix due to the high salinity and pollution levels.
Water testing is a great tool, but the ultimate water quality meter is the diversity of life living in the water. Once you establish the limiting factors of your local ecosystem such as predators, pollution, salinity, calcium, magnesium, trace elements, dominant species (algae etc.), lighting, water movement and temperature, you can adjust these accordingly in your private peace of ocean.