I know I can order the OEM washers online, but I'm too impatient to pay/wait for the shipping on them. Can you use standard copper crush washers under the cylinder head nuts or should I go with stainless/mild steel/aluminum/etc washers from the hardware store?

They are copper, for a good reason. Do not be cheap and try to make something work.

I used copper last time and they came out utterly destroyed, so I just wanted to make sure I put the correct type of metal back in. Copper it is then. Thanks guys.

Believe it or not ... destroyed is the indication they worked.
The yamaha XS stuff is steel and rubber on the outers, and steel in the inners, and we replace those with the GS ones which are considered an upgrade.

http://www.650motorcycles.com/277engine803.html

Scroll 1/2 way down the page.
Cool.
Buddha.