Sky Diver: I have absolutely no idea. I read somewhere that you could put ATA100 drives on Cable Select and the computer would happily work out which one to use. They would work just as well with the master/slave jumpers set. My drives are both on IDE3 to reduce the number of cables within the case. The advantages? I have no idea. The fact that ATA100 has specific locations for its master/slave drives on the cable kinda negates the fact that you don't have to worry about having one drive on master and another on slave if you use cable select.
Strike: I probably reinstalled Windows/drives/etc about 7 or 8 times before I got a stable system (which it is at the moment, thankfully). Fortunately it only took me about 20 mins to install the OS each time, plus I was determined to get it right (not entirely convinced it's right now, but never mind) so I wasn't too bothered about reinstalling all the time... The ACPI problem may have just been my combination of hardware (SB Value, GF2, USR modem). Perhaps Windows Whistler will sort all this nonsense out (it's kinda pathetic, really)...
Have fun
Tim