I'm new onto this forum so please bear with me as I've not read this entire thread but I thought I might share my experience with upgrading my empeg with you anyway. My upgrade process was using the Windows software versions.

Empeg / RIO rebuild with multi-drives

This is my experience during a rebuild with 2x 250GB WD2500BEVE drives on Empeg MkII (sn 080000452).

Using builder_bigdisk_v6.upgrade

both drives initally connected as master/slave

failed to find drives (bad pump) when both drives connected
unplugged drive on end of cable (slave) - then success

unplugged first drive - plugged in 2nd drive on the end of the cable - failed
plugged 2nd drive to first cable point - failed

changed jumpers to make 2nd drive master and plugged it back in on the end of ribbon - success

hence drive needs to be master to work, ribbon point not relevant
hence with 2 drives you must do them one at a time

Whilst each drive is plugged in individually and set to master then run the software installer.
hence for 2 drives you should repeat the process.
used car2_v2.01_hjack.upgrade

Note - even as Master the drive now needs to be on the first ribbon connection (not the end) or it fails

Once complete for both drives, connect both as master/slave and it works fine.
Capacity found as 360GB