That is huge. Are you really going to put controller flanks on it? Without them, it's already bigger than my PGPC, I think. And that thing is big. If you're doing a Wiikey, you might be able to fit everything in the original Gamecube case, and just add flanks on that. If that's the style you're going for. Assuming you relocate the regulator board, etc. Should all (including batteries) fit in there easily, with some modding.
But, well, if you want to stick with your current plan, more power to ya. Do what you want and what will be fun.