[dnanian]

Well, first, I basically disagree with the conventional wisdom. I always let Software Update update my system, and never use the Combo. I also don't obsessively repair permissions unless I have a specific problem that a permission repair will fix. (It's not magic, after all.)

As far as FireWire drives go, there certainly was a problem from 10.2.8 -> 10.3, if you had downlevel firmware. But, if your FireWire firmware is up to date (always check before an update), I haven't had any problems updating with my FireWire drive(s) attached.