I assume you don't have any fish in the tank right now. I would suggest just emptying all the water and starting with fresh mixed saltwater once you replace the silicone.
This is a new thread linked to my last one. I believe we narrowed it down to poisoning from silicone I used to seal my sump/overflow (GE Silicone II Window & Door).
Not sure if this is a typo but i believe that GE selicone II is the window and bath stuff. This has a mildew prevention chemical in it that will poison your tank for sure. You need to use GE silicon I. Also to answer your other question the silicon may finsih curing under water but i strongly suggest that you let it completely cure before you add any water. Often when something like silicon or glue is drying it releases things you really don't want in your tank. It can only be trusted to be inert once it has completely cured.
The liverock you can rinse in saltwater. I would take it out and put it in a container with fresh mixed saltwater and some high flow. This will help flush out all the water in the rock. I would say use RO
water but it would be hard to rinse it will without loseing all the bacteria from your cycle.
You can leave the sand in the tank and rinse that well with RO
water. Fill it so that the water is a couple inches over the sand and then get in there and dig it up real well. I would flush it again if you have the patience after it settles.
I'm sure it is tempting to try and reuse or clean the water you have in the tank now but i think it would be very difficult to properly clean and the risk of putting in more live stock and having it die again would be somewhat high if i had to take a guess. It just isn't worth the frusteration of losing more fish.
After you have finished all of this i would run a good amount of carbon in the tank for a couple days just to be on the safe side. Also put in another shrimp for a day or two and test your ammonia to see if your tank is still cycled after this ordeal. You do indeed have a long week ahead of you. I am very sorry for your troubles.
EDIT: sorry for repeating a few things you already knew. I just went back and read the other thread you linked to trying to figure out what the problem is. I have found that clowns are some of the most durable fish out there which is the only reason i can think of that they would survive and the rest wouldn't. Do you have a QT tank you can put them in for a while?