I just got the exact same setup - AP24 with the metal halide lights. I'm amazed that you call the fan in the hood super-quiet; it sounds like there's a helicopter is taking off to me. I'm seriously thinking of replacing the fans in the hood with something quieter - this tank is in my bedroom!
I am replacing the stock pump with a MJ1200; I also did the egg-crate plastic top idea that someone suggested on the first page of the "Aquapod Fun" thread. I also am planning on running a bakpak2r (protein skimmer and bubble trap thingy that hangs on the back). I'm not sure how well this is going to work, but I've read mixed reviews on the mini skimmers that can fit in the filter compartments.
Right now, it's full of tap water (checking for leaks!) I am planning on live rock in a week or so. I haven't decided whether I'm going to put rubble in the filter chambers, use the sponges, or exactly what I am going to do.
Are you worried about potential heat problems? I am. I was checking LFS's yesterday, and the one I liked best had two nano-cube 24s up and running in their store. They were drop-dead gorgeous. The woman who maintains them was showing me how she'd set them up - she was running a small skimmer in the filter tank, and was using some floss media in the filter inflow compartment. Other than that they were running stock pump and no additional powerheads. I asked about adding powerheads and was told it would be too much for such small tanks.
I noticed that they weren't using any heaters, which makes me think that heat issues and nanoreefs perhaps go together. I suppose I should mention that these were light-in-lid types of setups - we have a lot more clearance between the lights and the water. They did have the balasts for the lights hidden below the tank (a nod to heat problems I suspect.)
Anyway, I haven't even put rock #1 in the tank and I'm already thinkin of heat issues and second guessing myself. Perhaps I worry too much, but I really want to get this right.