Welcome to TBCS PCdeaf!
I'll try to give you some answers. First off, you won't have much trouble with wood as a building structure, it plays nicely with PC's so don't worry about the type except for which types are easier to work with and affordable. For some inspiration, type "wood" into the search engine on the right of the screen and browse through some of the other wooden mods to get an idea of what you are working with.
1. I can't say for sure but as long as you are talking about a small magnet with low field strength I think you'll be okay at 6 inches from the monitor. But I would wait for a more expert opinion than mine regarding this.
2. As for this, you should do some careful research before committing to build. I would google "biggest video card" or something of the like and see what dimensions you get to allow for enough room. And when you start planning your build, take a note from one of the pro's (CrimsonSky) and try making foam or paper mock ups of the equipment just so you can arrange them and measure.
Here is a good example of what I'm talking about.
3. Yes. The motherboard's are sized to fit standards, the most common of which is ATX You can find all of the dimensions and such on google for this as well.
4. I already addressed this, but again, any type is fine.
5. That is not something anyone can predict, sometimes I don't see anyone in there for days, and other times it's packed. Just keep an eye on the dialogue box under the title and see if anyone is there.
Good luck with your mod and don't be afraid to ask any questions you have as they arise.
Jon