I source pedalpartsplus.com for enclosures. For a few bucks they'll drill holes for you, to your specs. My first build I had them do the holes, but after that I tried it myself and it's not bad at all, aluminum is easy to work with.
Pencil mark the center of the hole. Clamp the enclosure to a table (if it's already painted use cardboard or something in between the clamp and the enclosure). Then just start with a pilot hole, then use progressively bigger bits. I use a step bit from Harbor Freight.
http://www.harborfreight.com/3-piece...lls-91616.html