I'm sure you're already referring to my x360 controller build for crossbred900, but just in case:http://forum.arcadecontrols.com/index.php/topic,128941.0.html
Of course that was a fairly standard control panel.
If he's working a thumbstick with his toe, I'm not sure a larger analog stick would offer much benefit.
Make note of EVERYTHING he has use of. While it's best to keep things simple because you're not going to be there to service it all the time, adding an extra axis or button opens up that many more games.
2.5mm jacks are the standard for accessibility accessories if you want to add the option for later.
Check around on prices before buying from a place that sells products for the disabled. Most times they price gouge since either insurance/gubmint is paying for it, or they know parents will pay it. The same bite switch that a sky-diving site sells for $45 is $100 at those places. There is probably a cheap way to make a suck/puff tube although that might make you light headed after a while.
If the kid can work a PC, introduce him to Steam. Crossbred900 originally wanted the controller for xbox360, but ended up getting heavy into steam. I'm not sure of all the reasons, but I imagine it was because of the variety of games and how cheap you can pick them up via humble bundle or discount sites.
I'm not sure I'd make it this complicated, but if the kid did get into steam there is head tracking software used by flight and race sim guys that could add some more functions. It uses IR LEDs on your hat and a wii controller.
If I think of anything else, I'll post it.