Replacing the master drive is pretty much the same as adding a second drive.

You should :
1) remove all present drives from the system
2) plug the new drive on the cable, making sure it's set to "master"
3) run the car2.empeg.upgrade utility.
NOTE : I've been told today by David from Empeg that this utility has a known bug : it shows an 0x20 error in in the middle of the installation. This ONLY happens with MK2a's (riocar players). The "original" Mk2's should work fine. An updated car2.builder.update utility for Mk2a users is in the works.
4) applie either the consumer or developer image to the harddisk. (if you want to copy the files from your old HD onto it, you'll need the developer image)
5) voila, you're finished. Add the second drive back. (make sure it's set to slave)

But most important of all, read the FAQ!

I hope you'll have less problems with it than I had, but in retrospect this was only because mine's an mk2a, and I see in your sig that you've got a regular MK2. You should be fine.

Riocar 58gig (48gig + 10gig IBM travelstar) S/N : 10101747 red