I built my own case out of aluminum, kinda a standard case but it let me pick and choose where everything went and I had my friend do a custom paint job.
For one of these projects you are going to need a ton of tools.
I have not worked with plexiglass as the support material before so I can;t tell you much about working with it but I will say this, Make sure you do a motherboard tray first! it is by far the most important part and then you can do your measurements from there. also keep in mind all the cable management you have to do and that the fans will sick inward.
go here http://www.formfactors.org/formfactor.asp for info on atx form factor so you know the specs for where the screws have to go.
Good luck, and be prepared to be frustrated. I thought that this would be a simple project but it took far longer than I expected.
