m> The root partition has to be in the first 1024 cylinders, right?
Nope, just /boot. Most people don't bother with a separate partition
m> Does /usr and /etc also have to be there, or does it not matter?
They can be anywhere.
m> Basically, does linux have problems with over 540Mb drives, or am
m> I doing something silly?
It doesn't. But the BIOS does. The stuff in /boot is the stuff
that has to be loaded by LILO using the BIOS, in order for it to be
able to copy the Linux kernel from disk to RAM before starting it.
m> Does Linux have to on the first drive of the machine?
No, but /boot has to be below the 1024-cylinder point with older
m> Is the solution as simple as swapping leads and having the Linux
m> drive as IDE1?
Start by loading Linux using LILO on a floppy. Get that working,
then think about messing with the hard disks.