Jessica, first of all, welcome to MacMod. As for re purposing the innards, there is a lot that goes into that. The first thing is going to be to obviously remove all the parts, and that's actually rather simple and should be pretty self explanatory if you are attempting a project of this caliber.
When you get the case that you will be working in you firstly need to think about layout and proper cooling. That is paramount for the computer to function properly. Aside from that, its really about aesthetics and getting it to all fit inside.
Without more details on the case you will be using or any other specs, its hard to give too many recommendations. Just plan carefully and ask any questions you might have.
"Fix it 'til it Breaks."
Jacob - EiC & Director of Technology Mac Pro Quad 2.66 - 4GB RAM 160 GB SATA RAID 1 - 650 GB Storage Quad 19" Widescreen LCDs Accessorized to the Hilt
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