Shroomie, your problems weren't brought about due to your liverock, it was your bioload. Although the possible die off from the live rock could've cause a "mini cycle," the problem was definitely in your # and type of livestock. They were correct in selling live rock to you because it is a natural filtration element in a saltwater system, the problem with your situation is you didn't add the LR first. Doing so first without any livestock will cause a tank to cycle by itself and you wouldn't have to worry about losing any fish. Adding it down the road like you did has the potential of causing a spike in your system. So if anything, the liverock HELPED your system, not hurt it. Fish only or reef, liverock is extremely important for a natural and healthy environment. As for the liverock looking the same, it will for a loooooong time. It takes a while for that pretty pink coralline algae to grow. Ich is definitely a pain. Search the forums I'm sure there are a million so called "remedies" for it, just be sure its ich and not micro bubbles sticking to the fish from your new skimmer! New skimmers are known for that and I thought my hippo tang had ich before i looked very close. If your convinced its ich,since you have a fish only tank, you don't need to worry about higher salinity for coral keeping so you can do something called hyposalinity in your tank. Essentially, this is just slowly dropping the salinity in the tank below what cryptocarion (marine ich) can survive in. Im no means an expert in hyposalinity, but like i said, read the disease section of the boards and you'll find good help there. Keep us posted and tell us how your tank is going.
P.S. How long a time period did you wait before adding each fish to your tank when you had them all? Was it done all at once? Also, do you have a quarantine tank setup? This would make sure any new fish in your display would be disease free because you could watch them for a few weeks after buying them and treat them alone if necessary, just a thought for the future!
-josh