Did the air line come undone. If not try to blow in it. Also check the recommended high for your skimmer. Sometimes when they are to deep they will not draw air.
I think the rocks looking that blue would be from it being a top down photo. It almost looks the exact color of a blue + bulb. Your pictures look way better than any I have taken.
I would not use tap water to cycle your rock. The rock will suck up and hold all the phosphates out of the water. Leading to an algae bloom down the road.
If your signature is still right a 29 gallon bio cube will not be big enough. I had one in my 120 and when it was fully open it was about 16" across. Trust me if it lives it will get to big.
I would do an external overflow on a peninsula style tank. You could either make it black or cover it it cabinetry. That way no plumbing would be seen and you can go tight to the wall. if you made it into the cabinet you could have the returns come through the other side of the tank.