1----? Windows explorer only recognises 698gb of the 1tb of hard disk space?
RAID 5 will chew up the disk space if you are using 4 HDD ? 5 is optimal and space beneficial however if you want it all or all(ish), run them as individual partitions ie drives or a stripe (note: these will optimise space but offer little or no redunancy/security).

2----? Vista only recognises 2814mb of the 4gb of RAM?
2814 MB seem strange however you will never see tha 4 gig because of the 32bit addressing constraints 64 bit windows will fix that. However you may be able to squeeze more memory out with a BIOS update ASUS isn?t the greatest for BIOS update but give it a try. (For Future Ref: Intel make the greatest boards with magnificent support)

3---- ?When attempting to install the latest nvidia 650i sli drivers, all i
get upon reseting is a momentary flicker of a blue screen and a crash?
Make sure you have plenty of power going into those cards. Any whimsical power nuance is gonna cause it to fail.
A rock solid power supply is a must. 4 HDD and 2x 8800?s and your going to need at a minimum a good quality 650 watt PSU like an ANTEC

4---- ?After installing vista, one of my main chassis fans have stopped working ?
(Again this is not Vista related ? Try power related ? Your board needs Juice!)

Stay Smooth