Nice use of my template.

First off, (why does it seem that I'm saying this so much lately?) don't angle the P3 & P4 sticks in. All original games had them mounted the way you do now. You want the stick movement to match what the on-screen character is doing. Up = up.
Have you bought your controls yet? Are you dead set on the Happs sticks and a Wico 4-way? Are Ultimarc T-Stiks 8/4-ways not an option for you? I grew up in the 80's playing with leaf sticks and honestly have no complaints with the T-Stiks. I guess it's more of a cost/aesthetics thing though, as you're gonna end up with some dead space anyways with this layout. It's not like you really don't have the room for the 4-way.
Unlike JAMMA's opinion, I don't think that your P3 & P4 are
too close to P1 & P2. Might be nice to spread them out a
little more if you can, but they don't seem unbearably tight. Have you mocked this up as a full sized template yet? Your top panel is gonna be shaped like the box?
I do think that your P1 & 2 buttons are a little close to their respective sticks though.
I'd probably bring the spinner down next to the trackball. It's a pretty long reach down to the buttons there. I suppose you could remap the games to use your mouse buttons though.
You got the top fire for Tron? If so, and you wanna stay more true to the original, you'll wanna get it over on the right of your spinner.
Personally I'd use switchable 8/4-ways for P1 & P2, dump the 4-way, move the top fire over to the right, put the spinner where the top fire is now, and move both of 'em down about 1.5 - 2 inches. Move the P1 buttons & P2 stick a little towards the center. And maybe move the trackball a little to the left if you're one of the types who feels he's got to
slam it as hard as he can in a game like Golden Tee. (Myself, I learned long ago that extra physical effort doesn't always = extra force exerted. The trackballs can only spin & register so fast. I can get just as much velocity outta using two thumbs on a trackball as someone who's trying to break the machine.)
I don't think they're in my original template, but I put pinball buttons on the front angles of the CP box I just finished. Sorta like a mirror of where your admin buttons are. With a plunger on the straight front piece. As for your admin buttons, if you're gonna have 'em on there (which I am a fan of), put them where they're quickly & easily reachable. Maybe on a bezel panel between your CP and the monitor?
Keep at it. Designing is half the fun (well, for me anyways.) And seriously, do a full sized mockup out of foamboard, or cardboard, or whatever. No matter how good it may look on the screen there's nothing that'll show you the truth better than hands on experience.