Flow is a big part of the problem. I wouldn't necessarily say overfeeding is an issue...you may have hit on part of the problem a few times when you mentioned the sand sifting goby. He isn't keeping the sand clean at all. In fact, he is making it more dirty. What they are sifting for is the organisms that live in the sand and whose job it is to break down extra food, poo, and other forms of detrius. The goby won't eat this poo and detrius, just the creatures that do eat it. This means this junk isn't being broken down as efficiently into a form that can be easily released into the water column for removal via the protein skimmer, etc. Instead, it is rotting in the sand bed and releasing nutrients to the water column in a form that can be immediately used by algae, etc. These organisms also live in the LR and serve the same purpose. If the population as a whole in the tank is dropping, or gone, due to the goby, then detrius collects more easily. The sand may look cleaner because it is being turned over more often, but that is also allowing left over food and poo to get deeper in the sand bed to rot on its own.
Increased flow will help as will using a turkey baster or powerhead to blow out the rocks. I hate to say it, but more manual cleaning is your best bet.
