If I am reading this correctly, I would like to make a few recommendations. Mainly from my experiences with my 40g. When I was having a full out algae attack (in your case a phosphate, nitrate, bad sand attack), I took a large tub and filled it with my tank water (undesturbed and removed everything to that tub). That included all livestock and rock and such.
Now, I scraped down the entire tank, (in your case remove all the old sand and left over water, then scrap all areas that need it.) Next put your new sand down, begin filling the tank with new water (same pH, salinity, temp) move the rocks and animals back into the system and complete the water change with some old water if undisturbed in the tub.
You should not get a spike because your rocks have kept all the beneficial bacteria in them. However, you are adding new sand that needs to colonize, so just do not add any more bioload for a while. I have done this a few times with no ill effects and it was in a full reef with lots of corals, fish, inverts, etc. In fact I do it often on my traveling tank to keep it clean.