not using a skimmer for the first 6 months is HORRIBLE advice, and I would say the main reason your tank is in the shape it is in.
You can get away with not using askimmer, but depending on stocking and feeding habits you need to change 20-50% of the water a week for that to be ok IMO.
Honeslty, i fmy rock looked like that, or i was given a system to fix that looked like that, I would pull all the rock out, scrub it and cook it. I dont knwo where the link lives on this forum and im not allowed to link other forums here, but search for posts by seant titled "how to cook your rock" and you will find the directions. its a pita but 6 months from now you will have a nice clean system instead of fighting this hole you have dug for the next year and maybe pulling out of it.