Make sure to post some screenshots when you are done!
I think that first you need a case. Just borrow one or be able to get to one, that is all you need. Get out a ruler and measure all the critical areas (the 5.25 bays, HDD bays, motherboard tray, PSU area, and alike) so that you can replicate that on your case. also, while doing that, note the screw hole areas (for you certainly need those too). After you get the basic areas down, then just try to plan how those areas will interact (either in a standard case fashion or you can make something weird up!). Lastly, just keep trying at building a case and good luck on that venture!
Somehow I don't think this is a cost cutting strategy though. Generally, building a case (I think) would cost more than buying one from a vender. Still, this may not be so, you'll have to look into it yourself. However, it could be a fun project an an awesome conversation piece.
It might be better though to buy a cheap case (as cheap as you can find) and then mod that case to your heart's content. All the basic stuff is done for you and you can then just remove/add whatever you want and reshape the case as you like. I have seen some awesome case mods and this may be an option for you (unless you plan on making a case out of solid oak, or alike... that would be an OC fire hazard I think...
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If you really want something exotic and still want to save money, have somebody else do it. This was a quick Google (so you can do better than this), but check out this link.
http://www.mountainmods.com/cgi-bin/display.pl?dis=info
5th paragraph down, they said they would build you any case you send them a sketch of. Might work out for you better.
So, to recap, try to see if modding an older case would fit your goals. If not, see if having somebody else building it is your cup of tea. If you still want to build a case, try to get a case to look off of and to get measurements. Lastly, good luck.
Some links, this is some motherboard measurments.
http://www.antec-inc.com/pdf/mb_3d.pdf
I wasn't able to find any case building articles (I seen hints of one, but the links did not work). However, I got to run, so that is all I shall type. Hope it helped!