Copying the data will take a couple of hours - there's no DMA etc on the empeg. Last time I changed disks I started one before going to bed and it was done when I woke up, so I don't have any precise timings. I wouldn't sit around waiting, but go do something else while it works...

I don't know if CS works or not... isn't there supposed to be an interruption of one of the wires in the IDE cable (or contacts on the wire)? Doubt that such an interruption is there...
I've always used jumpers and had the drive closest to the IDE header as master (mainly because that's how they come configured from start), but I don't think the physical position matters.

The master drive will be drive0 (aka /dev/hda) while the slave will be drive1 (aka /dev/hdc - on a normal Linux system it'd be /dev/hdb, but it's fudged on the MkII's to keep compatitbility with the MkI's that used two master drives, each on its own IDE channel)

/Michael