Good luck with the chaeto. I think there's a couple things you're going to be seeing happen in the next month or so. Your tank is extremely clean....not just in design but in maintenance of the system. Aside from there maybe being too much light for your LPS, they may have been in too low of a ULNS system to support them. That, coupled with the bright light could have hurt them long term. My fuge did well for the first few months of the tank being set up. Slowly the chaeto died regardless the amount of flow or light I offered. To this point, I have tried to run a fuge 3 times and each time the chaeto disintegrated.
Keep an eye on it. If it starts to melt a little each week, your system is most likely incapable of feeding it enough nutrient to grow, which is not necessarily a bad thing. You could always add another fish. In fact, measuring a .01 on your Hanna Instrument may be a telltale that it may die out pretty soon. There's no sense in feeding the tank more just to support the chaeto...unless of course you're interested in keeping macro algae displays.
Check out Dan Rigle's TOTM
http://reefkeeping.com/joomla/index.php/current-issue/article/75-tank-of-the-month. He has some good insight with respect to keeping a mixed reef with a healthy refugium. More often than not, the people that have great SPS colors, happy LPS and a macro algae refugium all at the same time are carrying single digit nitrate levels like Mark Polletti, Keith Berkelheimer and Dan Rigle. Running too low on either nitrate or phosphate is sort of counterproductive to the overall balance of these mixed reef systems. Within reason, the tank has to be fed well to support the whole "benthos" without reaching a tipping point. Dan's got a great eye for the little nuances of minor changes that he makes. If his colors brown on his sps while LPS look happy, he'll feed a little less and turn things around. Likewise, if LPS look unhappy and won't open and his SPS look pale, he'll up the feedings. It's really a see-saw affect in a mixed reef. You keep testing the highs and the lows in feeding, photoperiod, flow and water change volume until you've narrowed it down to what works for your system. You and I could have the same size tank with the same equipment, fish, food usage and maintenance. If we each have a different aquascape all bets are off. Flow patterns have just been the changing variable that could affect one system's success over another. That's why EVERYONE'S advice on this thread (myself included) should be taken with a grain of salt. Aside from personal experiences in our own systems, nobody else sees your tank's reactions and changes on a day to day basis like you do.
I was told a while back that with my two Vortech MP40's on full blast alternating reef crest mode in a 72" and 18 wide tank was way too much flow and that's why they weren't opening their polyps. After personal obserfvation and trusting what I was seeing I concluded it simply wasn't enough. I added two more MP40's and voila, polyp extension and happy SPS. When you study the habits, maintenance and equipment of the best systems on these forums you get a sense of what the majority of people at the zenith of the hobby do. None of them seems to rush their systems at all, and almost all trust themselves over their equipment every time. I still remember Steve Weast saying he didn't believe in a cleanup crew because he himself was the best and most efficient member of his cleanup crew. You obviously know what you're doing or you wouldn't have such a sweet setup and overall understanding of what's happening in your system. You need to trust yourself and not push too hard too fast.
I can't wait to see that tank in person. Maybe I should be looking for a smaller, sexier setup instead of the direction I'm heading!!