I'm going to build a custom neo arcade and need advice

Hello,
I'm going to be building a neo geo arcade this summer as a project and needed some advice as to what I should purchase. I've been looking around and it looks like buying a HGA or Super Nova is the way to go. Which one should I get and is this the right choice?

I have heard good things about the Super Nova. I would go with that, other options include:
1. Neo arcade cab
2. Neo Home System and !Arcade! converter
...that is assuming you want to go the route of MVS...

Depends how much you want to spend. I did the same thing last year, here's what I learned. Don't plan on building a cabinet yourself, it's just too expensive and chances are it will never look authentic.
It's worth asking in the newsgroups (rec.games.video.arcade.marketplace) about used cabinets in your area. I picked up a used Double Dragon cab for about $125. Then you can just get an MVS board (~$75-$130), plug and play, and away you go.
I recently picked up a Midway (Open Ice) cabinet for $400, and am very happy with it. It's much bigger, has a 25" screen, and the entire control panel comes off easily with 4 bolts. This way I made a "neo 4 button" panel I can swap with the "4 player" Open Ice panel.
Note that depending on what game you get, you'll have to do some control panel hacking. Drilling holes, buying extra buttons and wiring them up should be expected for a project like this. The re-wiring is all basic, basic stuff and is really easy to pick up.