The stuff on the sand looks like cyano
to me. That's caused by nitrates and excess nutrients in the water column. It would be best to get as much of it out as you possibly can. However you do it is up to you, but its more common for people to just vacuum it out. You could also use a fish net, and just dig under that portion of it in the sand, and when you bring it up, it will let all of the sand fall out, but will trap the cyano
in the net. That's the way i did it lol. The illuminous stuff just looks like some form of algae to me.. nothing to fret over.. unless it starts taking over your entire tank. The cobweb stuff you are seeing over the holes in the live rock etc.. is most likely just sponges. I hear that sponges just come and go in aquariums, and most of the ones that do appear, don't last very long. So don't bug out if you see spider webs in your tank haha.
Bubble algae is bad lol. But i know that emerald crabs love to eat it.. soo maybe get a couple? You should also be happy that, that crab you found was dead. If you look at its claws, they are black. Any crabs with black tipped claws are usually bad for aquariums. Eating fish, inverts, and corals if you have them. If he wasn't dead, you would have had to remove him eventually when you started noticing your livestock dissapearing lol.