Thanks for the quick response!
You're probably right about the acrylic. I've seen people with acrylic 1p panels for street fighter and the like, but those aren't permanently mounted so if you apply a little too much pressure, the whole unit will move rather than break. Ill probably just stick with MDF as my design is already drawn up with 3/4 inch MDF. I was a little concerned about accurately cutting the button holes and figured I could have a shop computer cut an acrylic panel.
As for the buttons, I currently have MAME set so my fight stick "select" is my shift key (and unless I'm imagining things it's working 100% as intended). Simply pressing select and any other button doubles the functions; For example p1 start is my start button, and p1 coin is done by pressing select+start. Instead of a dedicated "esc" button, I press select+left, etc. There are some emu's that will not be so easy, but there are joystick keyboard mappers that should fit what I need. I'll likely only run MAME, fba, and u64emu (MAME isn't fast enough on the netbook I'm powering the system with, otherwise I'd just go 100% MAME), so not too many progs to figure out.
Sorry for the wall of words... Any one else want to throw their two cents in on any of this?