It shouldn't matter which way you charge it. The Firewire route may be more efficient but I could just be making that up... Who knows...
As for waking up to it still charging, I'm assuming you're saying that you leave the iPod plugged in overnight and it still doesn't finish. Are you sure it's still charging and it's not just saying that you can't disconnect it because you haven't ejected it yet?
USB. COmputer vs. ac outlet. The AC outlet charges without an issue. The usb on the computer wasn't completed charging even aft 6 hours. Yes. I did a disconnect first.
Btw, if I don't disconnect, the charge time is also different? or as long as its connected it won't charge? Example: I noticed if I'm moving files over to the ipod (alot of files) after its done and I remove the ipod, I noticed the battery indicator is lower even though I had a full charge before I started transfering files. So it looked like the battery was draining when when plugged into the usb port.