You can get huge numbers of every different brick available on Bricklink.com. I've built whole sets (using various online instructions) by getting the bricks piecemeal from Bricklink sellers and saved hundreds of dollars from aftermarket prices on the sets. Bricklink can get you the pieces way cheaper than buying multiple sets at retail prices, and you can just get the pieces you need, rather than some pieces you need and a whole lot you don't. The Bricklink website is not a particularly user friendly interface, but you can get the hang of it after a while.

There are programs you can download (from the Lego website I think) where you can literally build your own designs on the computer. Then, you can go to Bricklink and order all the pieces you may need.

Certainly a big undertaking! Good luck!