Removing and reseating all socketed ICs is something you should definately do anyway, as those sockets have a bad habit of going intermittent over time.
It's probably nothing in the SCSI controller's settings (stored in the RTC which is battery backed up) as you said it works sometimes. Software does not really go intermittent :-P
You should use "SetBatt A" to clear the amnesia bit in the RTC memory anyway.
Pay attention to SCSI termination, this can cause transfer errors if not done correctly. Motherboard termination is enabled by fitting 3 resistor networks into provided sockets. Drive termination is usually a jumper or fitting resistor networks.
Also replace the 50 way SCSI ribbon cable. Those IDC connectors go intermittent when you least expect it. :-(
