I don't know anything about saltwater, but I did look at some of the standpipes that are used as I am thinking about building a sump some day. I think you will be fine, the standpipes that you described work a lot better than a plain tube where water crashes down (and makes a horribly loud noise!!). I wouldn't worry about losing Co2, unless you plan to inject it. I am envious of your wave maker! As long as it won't blow plants out of the substrate, you should be fine. At worst, just dial it down (if possible) or direct/spread out the flow so its not too intense.
Take a look at this thread:
http://www.aquaticplantcentral.com/f...ad.php?t=56594 Rlking is building a refugium/sump and has had great success so far! He will give you some good tips that you might want to try.
I have never played with a tank this big, nor have I used any T5s, but IMHO 8 36" T5 bulbs is the max I would use without going hightech and injecting Co2, for swords and anubias I would probably use 6. A lot of people think you need tons of light and Co2 just to keep plants alive and healthy for some reason, in the end just listen to what your plants tell you! Leggy, slow growth? Add a couple bulbs. Nice growth, but tons of algae? Remove a couple. Once the plants settle in and the chaos of a freshly setup tank dies down, it is easy to see what your tank needs if it is lowtech.