I'm in the same boat and doing the same thing with a Pac Man cabinet.
What I've done so far was to take a lot of careful measurements of the original control panel. then to start I added 6"s to the width (front to back, or from the screen out towards your body) of the panel. I then cut several cardboard templates to this size.
Next I drew a 1/2" by 1/2" grid in pen on the cardboard. Mounted the first template in place with tape to get a feel for how far it would stick out. It was liveable.
next I got the dimensions of the joystick mounting bases (3"x3") from Happs website and the dimensions of the pushbuttons I want to use and I skecthed a few different layouts in pencil on my template using the grid I made as reference for placement and such.
When i had a layout i was happy with (2 8 way joys with 6 buttons per player, a dedicated 4 way joy in the middle with 2 buttons, 3 admin buttons, and a player 1 and 2 coin up and start button) I realized I could cut my board down a little so it wouldn't stick out as far. So I cut 2"s off. my final panel will, at present, only come out about 4"s further than the original.
This is a good place to start and will let you play with different sizes, layouts, etc until you get something your happy with