So, you’re looking to take all the parts out and move to new case?
It isn’t very hard, you know how to remove the stock parts, so you should easily be able to move them to a new case. However, if you have snap-in buttons, you may have some trouble moving them from a metal panel to a wooden panel, as wooden panels are thicker, and work best with screw ins. But you could look into a case of arthong, they accept snap-ins http://shoryuken.com/f177/arts-hobbies-new-diy-acrylic-cases-now-available-237344/#post8919389
If you keep your PCB and barrier strip, it will be very easy to move them from one case to another. Simply unscrew everything, unplug the harnesses from the turbo panel (the PCB defaults to D-pad), and then mount however you like in case (arthong’s cases also feature PCB holders), then plug the buttons back into their quick disconnects.
Now, for start an select, you’d either have to have a way to mount the start/select daughterboard close enough to the panel and drill small holes for the two rubber contact buttons. But what I would do is get two 24mm buttons (sanwa or seimitsu, however you like), and a few .110" female quick disconnects (Lizardlick has LL Quick Connect, .110" Insulated), you need four, but I would recommend at bare minimum 6 (for some “oops” protection. If you mess up, you can’t really salvage a QD), preferably 8 if you’ve never crimped before, because I mess them up, even with nice crimpers.
I’d grab these wire strippers, because they are cheap, usually available at radioshack, and can also crimp RadioShack 8.5" 4-Way Crimping Tool - RadioShack.com
Now, take the start/select wires (grey and white), and cut and strip them. Then, once they are cut and stripped, crimp on your quick disconnects, and then attach them to your 24mm buttons. Then your 24mm buttons will now be start and select. I think it’s easier than trying to find an impossibly difficult mounting position for that tiny daughterboard, and 24mm holes are much more standard on cases than those start/select buttons.