Sorry about taking so long to reply to your post clboertien.
I'll answer most of your questions here, but if you want to mail me, or IM me or something to discuss it further, you're welcome to do so.
Anyway, what i did for lining up the mobo, was I built the case first, and then laid the mobo down where I wanted it to go, and then got a marker, and put it through the screw-holes on the mobo to make marks on the plexi. Then I drilled out the holes where the marks were. Worked like a charm.
The pci, and agp slots were a pain in the *** to get right. first I thought I would just have a peice of plexi that each rested on, bad idea. So I just got a peice of plastic wall corner, and made a bracket sort of thing that screwed to the case, and made the corresponding holes to the holes on the cards, and now I screw the cards to the bracket. (It's similar to the way a normal case works, I'll send pics if you want)
I used metal screws on mine. some of them are touching the desk I have it on, (scratches up the desk if you're not careful) that seems to pretty-much take care of static.
For the switches, I just used the momentary thing you talked about. I should probably make mine look more professional, but my watercooling setup prevents that from ever happening.
For the sides, get the strongest clear plastic L you can get. The stronger the better, because if they're no strong enough the case WILL WARP (I'm seeing a little in mine, but its just the way its positioned, leaning to one side)
I went to the hardware store with my exact measurments for all my peices, and had the guy there cut it for me. He did a good job, and this was better, because I knew that I would have havked it to death if I had tried it myself
Hope this helps you out, any questions, just ask