I was wondering about the headroom situation, too. Unless you have very small bantams (and even then) the chickens on the high roost (and they'll all want to roost there, no matter how cramped) are going to be really squished. Make sure there's nothing sharp or splintery up there on the ceiling that could injure their combs.
Personally, I'd make both roosts the same level, because this avoids squabling in the flock about who gets the preferred roost, and I'd lower both roosts to give adequate headroom, say 18-24 inches for standard chickens. That would mean lowering your nestbox, too, so that it's lower than the roost. I'm not sure if you really have room to do all that, though. A three foot tall coop is tricky for interior design.