I use a smaller 520MB driveon the built in scsi for my boot drive. I use that for workbench and nothing else. I have a 60GB drive formated and use it for Work: which works aout nice. Get the original smaller drive working with 3,1 and the use it to get 3,9 upgraded onto it. Then you can get the larger drive slaved and make it work.
BTW ( 2) OS 3.9 Pre-Install (reboot after) <--What is that?