Hey Keith! I really hope this fish does well for you, because I am so envious :wink:
First off, I need pics! It doesnt sound like ich with the size factor, and this is something I know you have seen plenty of. Lymph isn't always at the edges and is usually pretty easy to diagnose. It also doesnt move around like ich does... do the spots remain in the same place or seem to move around? The scratching makes it a tough call though. It could also be a fungus or a bacterial issue. I think you need to provide treatment and get him eating all in sync. Try and get a pic or shoot me a very detailed description (i.e. color, texture, change in size, number of spots, any other symptoms).
You're on top of water quality right? Stable temp, salinity.... The subtlest thing could throw this guy off.
Do not start hypo with the rock in the tank. It will definately foul the water.
Will he eat live brine? If so, it can be enriched enough to get him through a proper hypo or med session with no LR. I can dig up some articles if this is an option for you.