I wouldn't add the rock straight away. Leave it in a bucket with a heater and pump and keep an eye on your nitrogen cycle levels. If after a week or 2 you have no signs of ammonia, you could add it. The last thing you want is to chuck it in the tank and have an ammonia spike.
I'd just leave the fish in, you may stress them a little, but not to the point of doing any damage. Netting them, dumping them in a bucket and reacclimating them would be just as stressful to the fish, but more of a pain for you.
Lights off will be ok, as long as you can see where your placing the rock. Sounds pretty obvious, but you need to be able to see that your not gona squash a starfish or frag or something. In saying that, lights on is ok too, just make sure your corals are closed a little, you don't want any small pieces of rock falling on the coral, especially the exposed fleshy polyps.
I don't think disturbing a 2 inch sandbed will harm anything, maybe some input by someone else will help though.
Good luck!!