Heh, I finally gave this thing another go after a few years and found my own thread when googling for help...
I started over, running DiskPart clean in Windows to wipe the hard drive. Then I created a small partition on the drive using WinUAE and installed Workbench on it.
The A3000 still didn't boot from the drive just leaving me with a Kickstart screen. Then I added the "Delay start" jumper on the Acard adapter, and... it booted! I suppose the A3000 SCSI implementation is just slightly on the slow side during boot-up. In any case, the original SCSI drive can be retired
Now, to finally replace that cracked socket...