1. http://www.krylon.com/products/xmetals/ (Meant for metal, but when used on plastic gives you transparent color)
2.The actual Dpad is from a Gameboy Color, the little control module that it's in is from a Radica Tank Assault game.
3.Ebay. I was just searching n64 stuff and found a guy selling stickers.
I've gotta say, this turned out very nice. I'm gonna remember it, for sure, because of all that attention to detail. From the grape color, the nintendo stickers and the n64 logo, you gave it some love. Nice job!