1.)Those are just extra fan headers if you want to use them.
2.)Not familiar with that board's BIOS so I can't give a fair evaluation of it. If there's not a setting to boot to the hard drive, that should be it.
3.)MPS Table version deals with multiprocessing, but if you want, set it to 1.4.
4.)Lower memory settings run the memory faster, though you may not necessarily be able to run all these timings with stability. Leave them at the default until you get your system running up and stable before toying around with them.
5.)See #4.
6.)I leave mine at whatever the default is.
7.)I eventually turn off stuff I don't use (like Serial and Parallel ports), but you don't really have to deal with it immediately. Leaving that stuff on won't hurt anything.
8.)I really don't play with this either, however, if you want, I'd have it set for 75-80*C since that's looking at cooking the CPU.
9.)Not unless you want to overclock. Even then, wait until you've got your system setup and working properly. Then, if you want, you can go play with the overclocking.
Via 4-in-1 drivers work for any Via-based board, so just grab the latest. So long as it's integrated into the motherboard, the other drivers should work as MSI uses the same sound and LAN chips on their board series---at least usually. If it won't work with your board they will say.
I'll have to check the site and see what I can come up with.