Usually though, I have the luxury of cutting and drilling the box to fit the board, since I don't do this for a living. Hat's off to the guys who do things like fit 10 gallons of high-speed logic into a 15mmx10mm board for the latest consumer gadget, where the industrial design group have already set down the "thou shalt fit into this small and weird shape...".
In this case, I have a shape with holes and stuff that I have to fit the board to nicely drop into. A case of reverse-engineering the mechanicals.
It doesn't sound like there are any great secret techniques, other than figuring it out the hard way.