Well as you can see, there's no mention of the Western Digital anywhere.

Currently, you'll have the IBM as the primary and the WD should be the slave. It might or might not need a jumper to make a slave - depends on the manufacturer. You could try just a boot without the IBM (doesn't matter which connector) and you should see just the WD drive instead.

The drive should have diagram on it for the jumper settings before you go rushing to the store to get one.

Personally I'd set the new WD to be the primary (since it's the newer and hopefully more reliable) and the old IBM as a slave after building both drives with the builder image. That way if either drive dies, your empeg should still somewhat work although you might have to disconnect the dead drive.