One thing is obvious to me, the BakPak skimmer, its not nearly efficient enough to handle the load, they are way over rated from the manufactuer. You might want to concider a larger skimmer... Another thing may be the sleeper goby, they disturb the sandbed and it releases whatever detritus that may be present and the skimmer cant handle the load so it just sinks back to the bottom and decays causing elevated nitrates and possibly ammonia... I doubt more water changes will remedy the situation >long term<.