Use 3.5" illuminated dome pushbuttons from CoinOpExpress, they seem to work well, or blow $40 a pop on Sanwa buttons if you can find them for the most ridiculously arcade accurate experience you can get. (Seriously though you don't need it that accurate, really.) Controller spacing is 5.5" between buttons center to center, and 5.5" between the two rows, same point of reference. The buttons in the top row are aligned to the middle of the gaps of the bottom row, or if you prefer, think of it as shifted 2.25" horizontally.
Hope that helps. Just look at a controller while you're reading it if it seems confusing, and it'll make sense. 
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