Most people will concur you should go read up on how a machine goes together at a base level first, before going into details, as it seems your knowledge of game requirements and interfacing is a little lacking. Don't be tempted to jump in at the deep end just because you've seen loads of flash cabs on here.
Anyways, once you've read Saint's book (and the FAQ's on here), here's some pointers I stick with;
Layout: Decide if you will be happy with the cost/aesthetics of your panel; you don't want to have a monter panel with things in the way that cost you a fortune, particularly if you rarely use them. 4-player panels are great, but decide if you really need 4 players if multi-player gaming is going to be a rarity. Being your first build, it can get pricey really quickly and even beyond your skill level if you go overboard.
Sticks: Decide how often you will really play certain games before deciding on fancy sticks and trackballs etc. A lot of people jump straight into the expense of extra sticks and peripherals before thinking if they will really use them. Likewise, decide how you like your joysticks to 'feel' first as stiffness/clickiness/sturdiness varies across the board. Dedicated sticks aren't really necessary with switchable sticks available these days. Plus you may not notice if you are not a purist. If you're going with a 4-player panel I'd recommend a couple of 4/8 way switchable sticks for P1+2 and regular ones for P3+4, as the U360's still need physical restrictor plates on the base for a correct feel on 4-way games. U360's are the daddy, but can you afford the extra expense if you aren't going to see their full potential often?
Buttons: Don't go overboard. 7-button layouts are only good for regular Neo-Geo players who want an authentic feel. If you just stick with 6 you can still play those games, even if the layout isn't quite the same. Likewise, I'd recommend 4 buttons at most for P3+4, as few arcade games used more than 3 and most 4-player console games only used 4 (ie SNES Bomberman etc.). Consider having a credit and start button for each player though as some arcade games depended on it, and they double as convenient start/select button for SNES etc.
Interface: You will no doubt need an interface of some sort anyway, so I'd reccommend choosing one you can put ALL your controls through for programming/troubleshooting ease. For simplistic wiring, a mini-pac (or two if going 4-player) will help you out as they are pre-wired with quick connects. Adding trackballs etc is also easier with these. Most sticks and buttons with simple microswitches will connect to an i-pac easily. Advanced sticks may require extra power/wiring that you may need to factor in to your budget and could be a pain.
USB connectivity: If going with a simple layout and having all your controls through 1 interface, you will only have 1 connection coming from your control panel anyway. Some panels/software might have issues with USB connection due to power demands or non-USB software compatibility. If staying simple I recommend the PS/2 (keyboard) connection personally, but that's just me. Many people think an arcade control panel can just be pluggedin like a USB pad with no trouble, but it's a lot deeper than that.
Have fun with your first build though, and have a look through the FAQ's before getting to the specifics here.