hello Shawn, imbuggin, everyone-
I installed and maintain an aquarium very similiar in size to what you are planning. 96x30x40. It is filled with a mixed bag of corals. SPS, softies, clams, etc. I has two built in overflow boxes, each overflow has two 2" drains. Main pump is a te-7md I believe.
An ETS skimmer fed by a tec-5.5 pump. 2 tunze wavemakers.
I made for this tank, an enclosed aluminum lighting system that is anodized grey. It holds six 400 watt halides. The enclosures have tempered safety glass lens' to contain the extreme amount of heat, and duct work to exhaust the heat out of the building. The safety glass is essential when hung over acrylic aquariums so that heat is not transferred to the acrylic.
This is a similiar system to what I fabricated for imbuggin. Both are hung over 96" aquariums. imbuggin currently has stainless steel enclosures, but soon will receive his aluminum versions. I donnot suggest using stainless for a couple reasons, mainly because the stainless is much heavier than the aluminum, and also because the brushed stainless steel will still discolor and corrode from the salt and other elements in sea water. Also, aluminum will stay a bit cooler to the touch.
I would personally use 400watt halides over such a deep aquarium, especially if you plan on keeping any clams. The aquarium described above has had a couple clams for many years. They are getting quite big now, but they have really started to grow more quickly and with beautiful color since putting them under the 400w halides. They were under 250w halides before in the same size tank, they lived but they did not grow nearly as fast.
pictures of the described aquarium and lighting enclosures here>
http://homepage.mac.com/starpolyp/PhotoAlbum6.html
To avoid a long and borring post i will stop there, but if you have any questions regarding the set-up, filtration, or the lighting fixtures, feel free to ask.