For a test rig, why not use a much smaller joystick or Dpad - to keep it from sticking up so much. maybe one of those digi-key ones like people have used on their mini builds.
I've ordered a much smaller industrial joystick, the JLW was all I had access to in Sketchup. Here's the one that will be used:
http://www.farnell.com/datasheets/75512.pdfIt will only protrude 39mm from the lid. Compared to the JLW's ~70mm height with balltop installed.
Also, what about putting everything under the top lid rather than on top. Then either remove or flip up the lid to use it.
The dimensions and design of the box I am using would make this difficult. The lid isn't readily removable and only opens 90 degrees as is.
Also, I would have the jamma connector on a cable and able to flip out when needed so the board can lie flat on the work surface. With the connector built into the side, you may have to support the other end of the board while plugged in.
I'll be making my own JAMMA extension harness about 3' long. I won't be connecting boards directly to the unit.
Recess the RCA jacks. or put them on top under the lid. maybe the display could be on the underside of the lid and used bartop style when opened.
The onboard monitor is for testing purposes only. When the unit is being used as a supergun the display used while playing will be a much larger TV/monitor.
There won't be much room inside the box to have everything be internal. The power supply, isolation transformer, and video converters will take up a lot of real estate inside (along with the lid components' depth and internal wiring). But there will be enough room to store the various cords and harnesses (but I don't think I'll be able to store NeoGeo controllers inside).