The back of the heatsink directly behind the LED is gonna get real hot, so cutting out the holes for the switches and letting the board lay close to the surface may or may not work out in the long run.
If I were in your shoes, I'd just hit the Depot for a piece of aluminum bar stock and longer screws; slice off 6 squares, drill them and you have perfect risers to get things leveled out. (actually marking, drilling first, then cutting off squares would be easier)
Good Luck,
Mike E.