I would just let everything get use to the enviroment for awhile.
My rocks got all different colors on it for awhile. I loved the floresent pinks and greens, but most of that is covered with the different purple and green coraline now. The black, I'm not sure but it could be a sponge. If you have flow and light don't worry inless it is slimy, hairy, or bubbly.
For trates, 5 will be ok for fish, just stick to your schedule maintaince.
Your tank will change a lot over the next couple of months. Just enjoy all the new things. I love to use a flashlight at night and check out the night critters. You will be surpprised what you find. I still find new things and haven't added anything new in a couple months. try it.