1) Really to your like/dislike. I have my monitor very close to the glass - maybe 1/2 inch back (the bezel being the 1/2 inch difference). I like that, gets me up close and personal to the game. Many games were built that way too - but other games the glass is pretty far away... like Donkey Kong as an example, the glass is almost perpendicular to the floor yet the monitor leans back at like a 45 degree angle, so there is a lot of space. I would suggest going to an arcade in town and see the different types and decide what you like.
2) Take a look at my webpage on the left - besides the Sub I have 6 other speakers, 2 under the marquee like you normally do - 2 right about the control panel pointed at me and the rears I actually extended back behind me so I get a full "surround" sound going. I would suggest one of those last two options.
3) I used plexi, I like the idea of being able to clean it easily (as much as you try to avoid it, people's hands can sometimes be dirty/sweaty). And you also don't want the condensation from the sides of your beer dripping into your controls....
4) I went the easy method and added one standard fan that I already had to the inside, the type you can clip on a pole or something. I'll be the first to admit that it probably isn't as good as installing actual exhaust or (whatever the reverse of exhaust is) fans to the cab, but it does the job, it is whisper quiet, and strong as an ox. I've left an electronic themometer in there, with the cab on for days and the temperature never gets much more than room temperature in there.