Without Autobooting, the Amiga probably doesn't know there's a HDD there at all. You need a SYS:Devs Mountlist entry stating the device specs which is invoked in the SYS:s/startup-sequence at boot.
If you visually inspect the PAL jr pcb's and try re-seating any IC's on the PAL jr itself, ram card and SCSI card you might overcome any loose contacts that have developed over time on the cards which could be causing the boot issue. (?).
AFAIK Kickstart 1.2 won't autodetect expansion ram other than the 256k front unit. Something like Addram or AddFastmem is needed. Not sure what the actual command is. Kickstart 1.3 may be capable of it though.
