In words of one syllable or less, what do I do?

Assuming that you can put both of the disks in the empeg at once:

1. Unplug the 18
2. Install the 40 (as master)
3. Run the disk builder (to format the 40). This is why the 18 is unplugged.
4. Install a player developer .upgrade file (to replace the builder)
5. Plug the 18 back in. You'll need to jumper it as slave at this point.
6. Open a shell prompt using Hyperterminal or similar.
7. Issue these commands:

# rw ; rwm

This will remount the disks read-write.

# cp -a /drive1 /drive0

This will copy your music and configuration from drive1 (the old 18) onto drive0 (the new 40). It'll take a while.

# dd if=/dev/hdc3 of=/dev/hda3

This will copy your dynamic data from the partition on drive1 to drive0.

# ro ; rom

This will remount the disks read-only

8. Unplug the 18

I'm not sure how well this plays if you've installed any other applications, but it'll work with a stock player. No need for hijack.