I would look at getting a better skimmer for sure. An aqua c remora pro would be an upgrade over what you have. You could keep the filters, but only have filter floss or carbon running in them, and then make sure you keep the filter floss clean. You could also run Purigen and Chemi-pure in them, both of which I use and work good. As for the substrate, that is a matter of great debate. I use a DSB, while others use crushed coral, and still others use nothing. I would do some more reading on which one you prefer. The crushed coral shouldn't be affecting your system a lot unless it is full of food/poop. The phosphates are an issue, and probably getting into your system from tap water. Look to either use bottled water, which I started with, and then went to a RO unit. Without doing something about the phosphate, you will have some sort of algae issues. There are certain chemicals/media you can use to take it out as well.
Finally, do a couple of large water changes with water that has no phosphates in it. Good luck!
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