For what it's worth, it looks to me like the orchid may not be getting enough light or moisture. I could be wrong of course. The leaves are very dark and they look dehydrated. If it were me I would try to give it more light. I haven't had much success with phals planted in hydroton. I don't think it holds the moisture long enough. My favorite medium is coconut husk chips. If you're going to leave it in hydroton I would consider misting the surface of the medium daily. The bump could be scale or a bacterial infection. Usually I just use soap and water with a paper towel to clean it off the leaf. Don't worry about the root. Sometimes they grow through the leaf but usually they find a way around it. The plant knows how to do it better than we do. The bottom leaf will probably have to come off but I leave them until they're completely yellow before removing them. Good luck.
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