1 - I don't know if you had dreamcast or PS1 on that list, but really any PC that can run windows 7 should have no problems running n64 and earlier. In fact, if it can run XP, it is probably fine as well. a couple ghz of cpu and a graphics card that is even slightly better than base onboard graphics and you are probably gonna be just fine.
2 - If 4:3 is an option for you, then absolutely go 4:3. You are talking non "HD Era" games. it is gonna look and feel better on 4:3. There are really only a couple big reasons why people would want 16:9. One, because they are trying to toss modern gaming into their cab, 2 - availability. 4:3 is easy to get with a crt, and if you don't mind using an old crt tv or monitor, (or better yet get a real arcade monitor) you are gonna be just fine. If you are set on a LCD, then you are not going to find it so easy getting a larger 4:3 monitor. 19" and smaller are readily available, but anything bigger has been phased out. Used 4:3 larger monitors can be found.
16:9 also doen't fit as well in a cabinet. People either change the shape of their cabinet to fit the monitor, which can often look off, or they go with a much smaller monitor that doesn't fit the space well, which also looks off.
Some people compromise and get a 16:10 monitor. It isn't an ideal solution, but if you must go widescreen, go with 16:10 before 16:9.

3- The "universal" layouts are usually 6 button street fighter layout, or a 7 button layout, which is the street fighter layout with a extra button on the lower left row. Not that there are a plethora of 7 button games, it is mostly to accomidate 4 button games like Neo Geo and allowing you to use only one row to play.
One suggestion I would like to make is don't focus so heavily on the other features just yet. Pinball, console gaming, lightgun should be second banana at this point. Design a really, really, really good 2 player cabinet first. Make sure the exact arcade games you want to run will be fully enjoyable first. Then find ways to work in your additions without compromising the core of your cabinet.
