Wow, what a nice little thread this has turned into. Sorry for my absense--busy, busy, busy.
I might tend to get some new rock, maybe some aquacultured pieces, too, to maximize diversity and really get the substrates crawling.
I was thinking about that (especially the aquacultured stuff). Since I'll be transferring from one tank to the other I've not worked out quite how to do this--I really don't think I want to stick some new rock (even well treated aquacultured stuff) into the display, and I'm not sure my roomate would want another tank around for "curing". If I can work out how to do this I'd really like to add some of the Florida rock though. Have any of you guys worked with this stuff? What did you think?
Feed well (phytoplankton, and particulates (golden pearls type stuff), do water changes if required over the first six months to deal with the nutrients from feeding while the substrates get cranked up.
Absolutely. While I hate asking about certain specifics (reasoning and understanding is far better than following a recipe I think) what should I be looking for in terms of elevated nutrients? I'm used to getting undetectable for phosphate and nitrate (or at least <0.5 ppm nitrate) and anything higher would scare me I think

Should I just not worry if nitrate gets to, say, 3 ppm? I'm sorry to ask such a difficult question, but I anticipate myself 'freaking out' when I detect high disolved nutrient levels.
Lots of herbivory, mostly as snails.
Absolutely.
And, stock with a lot of coral after it is stable, even if it is coral you don't neccesarily want down the road. Things like digitata, Pavona, etc.
Now this is the part that worries me. I do already have several corals to transfer over, (some small, some larger). I really don't want to put any undue stress on any of these. I recognize that the environment will be destabalized for a period, but I'd like to minimize that as much as possible. It really breaks my heart to lose anything. Oh, and I think M. digitata and Pavona are absolutely lovely corals
I would limit soft corals or things that have lots of secondary metabolites unless you have a little carbon area built into the tank.
Ha, not an issue. Frankly, I'm almost afraid of soft corals (in the context of an aquarium) now. I had a small tank (~10 gal.) as well until about 6 months ago. I had several corals do very well in it. After I added a large Cladiella sp. that was all I could keep in that tank. It damaged some Ricordia florida, some zoanthids, and a few other Alcyonids. I liked it a lot, but that forced me to learn respect for their potency. Anyway, long story short I don't plan on adding anything like this to the tank. No nasty algae either...Caulerpa, yuck!
Then, when the tank is ripping after about a year and you are getting it stocked the way you want, make sure to use a lot of live foods like artemia nauplii.
Absolutely.
I think you'll be really really happy with the way it turns out.
I think so too!
Now for a few follow-up questions.
I realize that this system simply is not going to respond to large food additions at first, but over time will be able to utilize quite a bit. I am going to have to feed the Banggai's (the male has eggs in his mouth for the first time as we speak--I'm beyond excited

--at least second generation captive bred) as well as the Tubastrea, though I don't anticipate them producing God-awful waste and totally disrupting the system. At least I hope not. For everybody else I plan to use cultured phyto (DT's or maybe something from Reed mariculture a friend of mine has been trying), Cyclopeeze for everybody that can eat it, and Golden Pearls for all the really little mouths. Also, I've never used Golden Pearls before--I'm more used to 'wetter' food--so I guess I'll have to experiment with amount used. To finally come to a question: do you see anything inherently unbalanced about what I'm planning or anything you think will trip me up?
Now as for the corals I have. As I said, I really don't want to stress anything (or especially lose anything) if I don't absolutely have to. I can, however, transfer things over the course of a couple of weeks. Hopefully this will allow the substrate (both rock and sand) a little time to get going before I really start putting much of a demand on it. Anyway, have you any suggestions as far as actually transferring all the corals over without a hitch?
As far as IA, yes, very impressive tanks. That has to be the neatest place I've been off an actual reef. What impressed me the most I think (it's so hard to pick one thing) is the way the tanks looked and felt alive--the way reefs do. They didn't seem like all the big-skimmer tanks I've seen. They didn't even seem like my well-fed-attempt-at-biodiversity-with-a-skimmer tank. Like you said, they are the closest thing to an actual reef I've seen in a closed system. Other than that: big fat tangs, big fat clams, big fat urchins, and big fat corals
Another thing that has really motivated me is my girlfriend's tank. It's been up about 6 months (about 15 gal.) has pc lights, a couple little powerheads, and most of all no skimmer. She has some happy growing Xenia, a very quickly growing Euphyllia paradivisa, a shrimp and little Allen's damsel. The thing that sets this tank apart though is that this tank (unlike any other I have ever helped with) also has marine snow

The rock is becoming just covered in all sorts of pretty algae, there are tons of worms and brittle stars, and sponges are begining to really get going. The tank looks a lot more like a reef than my tank with it's purple/red rocks that occasionally have feather-duster worms, or small sponges growing in some tiny nook. I find myself spending more time looking into that little tank than my own.
Anyway, Eric I very much appreciate your time. As always I am in your debt.
Cheers,
-Chris