I have lots of experience from upgrade/downgrade all the time.
This is all my tanks from w/in the last 2 years, and 3 months.
http://www.swt.edu/~xp42012/

I don't think you're going to have problem w/ the SA tap water. Did you let it evaporate/dry out b4 you add your salt water? The scale is probably just calcium. HOw much Kalk did you dunk in?

When I upgrade my tank, I usually try to sell off as much of the old rock and corals, fishes, livestock as possible.

I would mix the saltwater in separate containers. Put the sand down, aquascape the tank w/ the LR. Then slowly pour water back into the main tank.

W/ your current situation, you might want to put some cured or uncured LR in there and wait until the sand clear. What's going to be hard for you is that the sand will get cloudy over the next several months each time you try to aquascape your tank. Each time it cloud up after the sand is laden w/ bactera; it will take about 3 hours to overnight to clear out from you messing w/ the bottom rockwork. I have cloudy tank all the time that doesn't seem to affect some LPS & soft corals, but I don't know about SPS vs. cloudy tank since it's a new field for me.

That's why my newest tank is going to be a bare bottom, I like to reaquascape all the time, and the sand is not helping out w/ their incessant clouding up.

Flosss & a good skimmer can help to remove the small sand particle. But I usually like to keep all of my smaller sand grains if I can. Which might explain why my tank get cloudy alot when I rearrange the tank.

As for the water, I've used up to 80% new water, 20% old water w/ no problem. But I usually mix my new water up for a long time b4 I would put it to use.

This is just basic answer, if you have more question, please let me know.