Yeah, I used a slikstick blank as my first panel, with hardware I'd chosen. It did *not* like the screws at all, my IPAC was hanging by a thread, and nothing was very tight. I'm not a fan of particle board at all.
If it helps any, the last time I touched a piece of wood was when I was 8 years old pounding random nails into discarded wood from my father working on stuff.
In the last couple of months, I've been building my own panels without any major difficulty. I give you my word, it is not at all difficulty, especially if you do the research here and ask questions when you're not sure. I spent $35 on a corded hand drill, $35 on a jigsaw, and bought a router for $50(Still trying to figure out how that thing works, lol). The MDF boards cost me $9 apiece. Bits are cheap. Fostner bits for drilling holes make the thing incredibly simple(Protip: Drill a small guidehole before using the fostner bit, it actually makes a huge difference in how fast it cuts).
For cuts in the middle, use the fostner bit to drill a hole, then just jigsaw out pieces to get the shape you want. (Trackball, flightstick, driving controls)
Measuring is easy, once you have the height/width of the panel, find the middle and mark it. That's where your joysticks will sit. The buttons for a neo-geo setup seem (IMO) most naturally to be ~2.5" from joystick and 3/4" above/below midline, with 3/4" in between(Can go down to 1/2" for smaller hands).
There's a number of different patterns, this site gives a good rundown...
http://www.slagcoin.com/joystick/layout.htmlAs far as countersinking goes, there's no reason why not. Wouldn't be too hard to do.