[Symbiosis]

You didn't mention a protien skimmer. With your fish load and desire to have a system with more corals, IMO a skimmer is a must. It should also help with your algae/ammonia problem. Also, do you use RO water or tap water for changes and top off's? If your tap water is high in dissolved matter, algae can grow pretty quickly. I think your best course of action is to remove the undergravel and substrate, put down an inch of oolitic aragonite if you just want it for looks (4" if you want it for nitrate reduction, which I don't think is needed if your nitrates are already 0), clean all the bacteria/algae you can, do some water changes and wait for things to settle down. I say remove your current substrate as it's large grain size traps more detrious than the fine oolitic. I think this will help with your ammonia problem at the same time removing the algae/bacteria's source of food.

Oh, and for a skimmer, the Aqua C Remora is the best hang on you can get in todays market. Might cost a little more than say a Seaclone, but its performance will more than make up for its price.