For a class project, I would suggest spec'ing Pro Tools Native.
I would justify that position (which software) based on industry standards.
It would be silly to spec anything else for professional purposes.
That said, With that Mac, if budget allows, you could spec HDX1 and Mytec boxes with a minimum of 16 I/O (Preferably 32)
OR, if the budget weren't to allow for that, you could go with HD|Native and HD I/O's, or Lynx/Apogee, whichever fits the budget.
(Don't rule out spec'ing used equipment, if you are allowed, it will drastically reduce your budget, look up AltoMusic or GSharpMusic on ebay, they almost always have bundles, or at least a bunch of Avid hardware)
Also - DO NOT spec HD, Core, Accel, Process Cards. It is old generation and will be obsolete with the release of 11, so that would be a horrible move.... also, same goes for the Blue/Silver interfaces, stay away from them too
You should get a good clock. Apogee has great stuff but it may not fit your budget. I would stay away from Digidesign Sync, while it isnt terrible, it is likely to be updated and dropped. If you need something budget, call Black Lion Audio. A good clocking source is important for high end audio.
One last front end point, in most cases, unless you have a large high end console, you don't generally need as many outputs, so 32 in and 16 out would be great.
Control surface.... this is going to be a tough one. You NEEEEEEED a surface.... for professional workflow it is a must (Being able to ride faders against each other in a mix is priceless...)
I would suggest at least 24 faders. Anything less becomes restrictive in most mix environments.... if you've ever worked wtih 24+ you know what I'm talking about.... the more faders you have in front of you the better..... Can't tell you how valuble it is to be able to change, say, lead vocal and snare levels against each other at the same time without the need for VCA groupings or having to shuffle track positions around.... so more faders is not only going to help many people improve their mixes, but at least drastically speed up their workflow.
Tascam US-2400 is the cheapest thing I can think of right now, and while it is unofficially 'supported' currently, it is hard to know whether it will be in PT11, but I would be amazed if it wasn't cause that would mean Avid dropping HUI and I don't see that happening.
While it is a low end board, it will definitely suit the function you need and should allow you to put the bucks where they really count with the other equipment. Remember, while higher end controllers are great, they are not as important as your converters, etc. (I've owned pro controls, control 24's, a D Command for 2 weeks, and I've worked on almost every Icon, a few SSL's, Harissons, etc)
Accoustics..... year. As already mentioned, stay away from parallel surfaces wherever possible, and if you can, wave your ceiling. Or at least structure/slope it... but while this is a spec assignment, I would wave it - look it up. Also, you can work with a slew of materials. You don't have to be all absorptive. Go for some extra cred and really research this part, cause you could have the best equipment in the world, and it will still sound like crap in a poor environment. You can use accoustic foam, diffusers, wood (I love rough sawn cedar, it sounds amaxing), wood or poly block arrays (Another thing I am fond of, and I mix/match em with accoustic foam), Cultured Stone (Man made, looks like stone), etc. The trick is keeping the room diffused where it needs to be and absorbed where it needs to be.... you don't necessarily want a room completely 'dead' - but there are literally novels on this stuff
Mics... I'll only briefly address vocals, but I'm particularly fond of Neumanns (70's U87 in particular, but also like the TLM149 and the budget TLM103), Violet Design / JZ Mics (I demo'd their line before it was for sale in the states, and their mics are amazzing!), and some of the Blue line (The higher end ones..... nearly all designed by JZ's company)
Cables - Cables will always sneak up n get ya. Spec for built in 'trough's' in floors walls or ceilings (Floors and walls best if you can) to channels or patch panels in proper positions (Behind consoles/racks, and in booths and machine rooms) and spec for Gepco or Mogami cable.... Gepco will save you some bucks, and it's great - SNAKES, install cable.... as many channels as you need for each split. Ends.... Neutriks suffice as they are good ends and good price.
Spec a machine room or whisper/iso (isolation) 'racks' .... the small climate controlled room/closet that your interfaces. That way you don't have the fan noise of your gear in your mix environment.
Monitors (Speakers) ... Spec for NS-10M's for nearfield, a great sub, a surround setup (May as well go 7.1, blue sky has some good deals), sppec some mid fields, and spec some farfields to build in to a 'soffit' in front of mix position or in the wall in front of it.
Windows, be sure yo double pane and slope - just look it up.
Just figured I'd throw in a couple things. Good luck