I agree with Reef Bass, they look overexposed on my monitor. I have had problems with the built-in meter on my D700 overexposing coral pictures, and the meter in your 7D should be no slouch either. Check your metering mode (spot might work better than matrix) and make *absolutely* sure you have RGB histograms enabled in review. The camera will expose based on luminosity (luminance histogram) but you could be totally blowing out individual RGB channels (very likely since corals are very colorful). If you are shooting in anything other than manual, the camera is going to expose for luminosity and you will blow out one or more of the RGB channels most of the time in my experience.
I would kick it into full manual, make sure RGB histos are enabled for review, and shoot for good RGB histos instead of for a good luminance histogram. It's OK if a color channel or two clips a little, because hey it's corals, they're colorful. But making sure they are only minorly clipped if at all will also pull the overall exposure down and I think you'll get images that look more natural.
As for the focus issues, that's just macro photography I think. I don't have a true macro lens and just use my 24-70 which has a little under 1.5' close focus distance and a .25x repro ratio if I recall correctly. Anyway since I haven't gotten my macro lens yet I can't really give you any practical suggestions, other than the basic "use a tripod" type advice.