You could try draining most of the water out of the tank rather than moving the rocks. Create a depression in the sand; the fish will end up collecting in the low area and you should be able to just pull them out. When you're done, you can pump the water back into the tank, having disturbed nothing. A short time out of water won't hurt the rock or corals. I learned this method here and used it on my 30g. I found that it was quick and easy, but would be more difficult with a 90g. If you have a few big containers and a strong pump it should be feasable.