Hey, so long as I am not tired I am a fan of long posts - it shows the person puts a lot of thought into what is said.
Glad you like the suggestion I made about the PC Mod - I've been wanting to do an entertainment center mod with a similar idea of having two computers (one as a server/MP3/MP4 converter, one as the front interface, complete with game emulation), but money and time have always been at war with me. (The economy couldn't have gone south at a worse time! LOL) Maximum PC and CPU, both PC magazines, have a long-standing relationship with Modders, and both used to showcase a mod-of-the-month in the pages of their magazine. (CPU - short for Computer Power user - still does.) It's worth going through their archives to see what others have done; in the same book that made me think of that desk PC was a person who built their computer inside of a working aquarium. Hope no fish or motherboards died there!
One mod you may want to look for as far as a dual-machine setup is a cube mod where someone put two computers into one machine - again, similar concept to mine, but it was built within an existing cube-floor server. I don't have any info at hand to help you, but my gut feeling is that one of those two sites will have it. (If I recall, I saw it a few years ago in Maximum PC.)
Considering how I've seen motherboards and hardware mounted, unless there is some weird reason (such as oddball liquid cooling setups, which would be rare, especially on the Mac), mounting it sideways, upside down, or any way you wanted to should be no problem. (You could probably look at mods on this site to see it!) Just make sure everything is easily accessible when you need it and that there is proper ventilation for the heat.
As much as I like the idea of a built-in screen, I would advise against this, especially if the source for the screen is what I think it will be. (If I am wrong, please correct me on this.) A lot of laptop parts are proprietary, and even when, such as the graphics cards, they follow the same standards, manufacturers tend to mess things up enough so that only the memory and hard disk are upgradeable. If you should decide to use the screen in your Macbook on a newer machine, you may find hooking it up to be difficult.
Even if you're using an external screen it'd probably be better not to break the screen out of its molding. Instead, I'd suggest using an LCD Mount that you modify to get the screen-rising-out-of-the-desk that you want - keep the part that attaches to the LCD Normal for future use and upgradeability.
There are two other ideas I could suggest, as far as screens. The first is a dual-screen setup using the built-in screen, since it sounds like you're going to build the MacBook Pro into the desk. (If you're not, I'd handly suggest a docking mechanism built into the desk so that you can still utilize both monitors.) The second, though, is to either buy a Touch-Screen Monitor or get some touch-screen film - especially if you do my first idea. With the amount of work being put in those technologies now, and the number of different ways it'll be put to use, it'd be a step up towards the future.
As far as the ports, great idea, and another place for suggestion: dig through the junk yards. A lot of computer manufacturers have implemented the ideas you want to do, and it'd be easier to use one of those mechanisms than to build it yourself. (Plus, it'd be way cheaper than to steal it from a newer tower, as far as cost!)
Finally, as I said before, build it to your needs - in other words, it sounds like you should put your ports to the right.
Keep me updated - sounds like a good idea.
-- Since you updated while I was writing this, I'll take the time to give a quick response: there may be solutions through NVidea, but the cost of doing them (and having them work within reason) may not be worth it. One solution would be something such as a USB-DVI hook-up, though (as you can imagine) the display response may be slow - it depends on what you want to use the display for. (The solution's good for small touch-screens, though - one of the things I am considering if I decide to do a carputer.) The best advantage to the USB-DVI is the price: the adapters can usually be found for less than a hundred, whereas a dedicated external graphics setup would cost in the thousands.
However, since you said you were possibly doing two machines, there is another solution: Software exists that allows a machine to be a dedicated second monitor (great for older laptops and people wanting to build 19-monitor setups - don't ask.) I don't know if there is Mac-compatible software, but one of the two mags I've suggested recently (as in the last couple of months) had an article on doing that - I'll post a link as soon as I find it.
Speaking of links, I figure this would be handy: Amazon has the book I've been pulling the modding info from, and even though it was published back in 2005, its ideas and advice is very sound for hardware mods, even today. It's called "Maximum PC's guide to Extreme PC Mods":http://www.amazon.com/Maximum-PC-Guide-Extreme-Mods/dp/0789731924.
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