After a few months of diong nothing, I decided to do some research and get this project over with already. As of right now, I just need to order a motherboard, some RAM, a CPU, work on the cabling issue since I'm leaving the original working of the power buttons etc... intact (if you don't know what I'm talking about you'll understand in one of the links I provided), and mod the I/O panel, and I'm done

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First, I had to buy a dremel. At the Home Depot I found this for about $35. You're going to use it a lot.
Next, I had to buy get some spacers to hold the motherboard down. $5 got me these, and if I paid too much, too bad. I needed them
Now that you have that, go get your drill and a 1/8" (3.175 mm) bit. You'll use it to make the hole where the new spacers are going to fit. If you use a bit larger than that, the hole will be too big. Better tight than loose,
if you know what I mean. I used the longer spacers everywhere except where the PCI slots are. I use the shorter one there because the area is slightly elevated.
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You're going to remove all the old standoffs/spacers from the case. I circled them in red. It's goint to be annoying and dusty, so do it outside. You'll go through about 20 discs (the dremel kit came with 36).
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Before making the holes in the case, you need to make measurements, remember? I placed a NIC card on the mobo so that I could line it up to the slots and not risk anything stupid. Also, since the mobo I used was dead I ripped off the parallel, serial, and vga ports because since they protrude you won't be able to have the mobo flush to the case. You'll understand when you try it. REMEMBER: be patient! Measure 10 times, cut once. Heck, measure while you're cutting!!
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After the ordeal, you'll end up with something like this. I used the dremel to make areas around where the spacers will be so that the door mechanism could slide perfectly and also so that I can just take off the plastic-door-mechanism-thing if necessary.
Once everything is in nice working order, the inside should look good and feel great to look at, as well as feel sturdy.
http://www.hardocp.com/article.html?art=MzUx and
http://www.hexus.net/content/item.php?item=617&redirect=yes helped me out A LOT. One is a step by step on how to do everything, the other is just shots of how neatly he organized the interior.
Well, I hope that this thread was useful. What I wanted to accomplish is to at least make it accessible to anyone interested in such a project. The fact that I only found those two websites depressed me, so I figured since it'll be here it would make it more public, and thus making me sound more redundant...? Before I start repeating repeating myself, thanks for checking out this thread. Hope you liked it and inspires you. ZOMG teh cheeseeniss iz c0mingz....
Think different
EDIT: Forgot to mention that when the project's all done, I'll have final pics of the setup and specs
