I recently went through almost exactly the same thing!
I had alot of algae because the guy I got mine from used tap water, most of it went away when I switched to RO
water. Having an RO
machine would be helpful, although I just use five gallon containers at the water machine in walmart. Using tap water is not the best for your fish but most likely they are fine, using RO
water just makes it easter to keep your ph and alkalinity under control.
You do not need a bubbler, it will just increase salt creep and evaporation.
Since the fish are too big for the tank, I think it is best to trade them to your live fish store. Doing this will free up your tank to do your substrate change without any fish to worry about. Also when you add your live rock, you will probably have a"mini cycle" due to die off on the rock. Having no fish would make this easier for you.
About a week after I moved my tank home I changed from crushed coral to sand, what I did was,
Siphon half of the tank water to a 45 gallon rubbermaid tub, (I have live rock) so I move all the live rock to the tub,I moved the heaters to the tub, attached my filter to the tub (this keeps the tub as much like the tank as possible for your fish, also it keeps the beneficial bacteria alive I'm your filter) I hooked up a power head in the tub, I caught all my fish and placed them in the tub, then siphoned out about half of the remaining water into the tub, after all of that, the fish could stay in that tub for hours with no problem. I then scooped out all the gravel with a clean dustpan, and cleaned out the tank thoroughly (don't use any soaps) I also used this chance to scrape all the glass clean, I rinsed my sand maybe twice with saltwater. I put the sand in my tank with about half new water at the right temp, along with another heater, now I waited about two hours for the sand to settle, then I put everything back into the tank (fish last). It all took about five hours.
Wow I said tub alot lol
As you can see this change would be alot less painful without fish. You would just siphon out the water in a tub, change out the substrate and put the water back in, then add your live rock and wait until the tank stabilizes. Then you can stock the tank how you want with the right size fish.