Planning, planning planning.
No matter what you decide to do, you will want to revise some things as you go along, to better accomodate the games you play.
Are you building a desktop box or a cabinet?
A couple points I noticed:
1. I like the sanwa joys, my biggest complaint is the mounting... they have no plate posts, so you always have those bolt heads showing on your control panel. As a purist, I like mine flush mounted, with the plate hidden by an overlay.
2. Pushbuttons... I originally had microscwitched pushbuttons like your plans, and ended up switching mine out for leaf switches... for games where rapid button pushing is required, there's no match for frequency potential.
3. If you think you may ever want to add led, trackball or spinner, consider using ipac's uhud instead... ultraversitile... does the work of multiple interfaces (so in the end is cheaper) and is no more complex (just looks like it would be).
Take a look at my cab blog, I go over a bunch of lessons learned and regrets.
Hope that helps.