New tank...Need lots of help

Sand is the most widely accepted substrate for a reef tank. If you change, you'll be much better off removing what you have and going with 4"+ of a finer sand. While I don't know anything specific about the goby you want, many gobies dig and some even sift the sand for food. If it likes to dig or sift, you'll want a much finer sand substrate than what you currently have. Digging can lead to problems with rock slides, so you'll want to place the rock very deep into the sand, if not directly on the bottom. If you are concerned about creating pressure points on the bottom of the tank, you can put eggcrate (plastic lighting diffuser) between the rock and the bottom glass. Some people that do this put a sheet of eggcrate in the bottom of the tank (covering all the glass), while others cut the eggcrate so that it is only under the rock itself.

Your live rock will do the bulk of the filtration, but the Aquaclear can be good for water movement and any carbon or other media you choose to use. Some people convert HOB filters into mini-refugiums and grow macro algae and pods in them.

There's many ways to do things in this hobby and still end up with the same result. Everyone has their way... the best thing to do is research, way the options, then decide what is best for what you are trying to do.

You can get eggcrate at HD or Lowe's. It's easier to find at HD (fluorescent lighting aisle), but many people have claimed to bought it at Lowe's (although I've been unsucessful at the one by my house).

When you take out your other substrate, you'll undoubtedly take out some of the live stuff. If it was an active tank with fish and inverts, many people would recommend changing out portions of the substrate each week, say 25% of it each week. Since there's nothing else in the tank other than the live rock, I wouldn't be overly concerned about the amount of living organisms you'll be losing. Most of the bacteria and tiny critters you'd find in that course substrate are living in / on the live rock as well. As long as the rock stays wet in sw, you should be fine. If it dries out or is exposed to the air for a period of time, you'll start to lose some of the organisms from the rock.

It's really not important how long ago the LR was harvested, unless it was dried out sometime since then. If it's always been wet and kept at a reasonable temperature, the bacteria that will act as your filtration will still be there.

You do not want to endlessly rinse the sand. You want the finer particles. I'd suggest doing as the second guy described, although there's people that would suggest not rinsing it at all.

Do you have a large enough cooler / rubbermaid container (that's uncontaminated) to put the LR in while you change out the gravel to sand? If so, you'll want to put the LR in it along with enough sw to keep it submerged. It would also be good to put a heater and potentially a powerhead in with it to keep the temperature up and water circulating, if possible. I would highly recommend doing this to prevent the finer sand particles from clogging the pores of the LR during the change over. The porous nature of LR is what makes it so beneficial and clogging the pores with fine sand particles would be a bad thing. There will be a sand storm for a period of time when you add the sand to the tank. Depending on the sand bought, it could be a couple of days before things clear up. It will be a frustrating period of time waiting for things to clear. If after a couple of days the tank is still cloudy, you could put a fine filter pad in your Aquaclear and run it temporarily to collect any remaining "dust" before putting the LR back in the tank.

I doubt the hermits will die from removing the gravel. If you find any off of the LR, just toss them in the same cooler as the LR until things settle and the LR goes back in the tank.