Yikes, this is a tough one. I don’t have a definitive answer, just some more questions or lines in inquiry to investigate. It sounds so much like a termination problem but you say you’ve accounted for that...
SCSI2SD configured correctly via attaching to PC USB?
Is the machine otherwise working? No latent battery damage? Power supply confirmed okay? Was the machine working before upgrading to 3.2? Tried a different SCSI ribbon cable?
How is your RAM configured, e.g., on which boards does your RAM live? 512K of Chip seems low - don’t most 2000s have 1MB onboard? Or do you have one of the old German motherboards? I’m guessing some RAM is on the 2091 so it’s probably worth running the 2091 RAM Test to make sure the chips are good.
Mask and MaxTransfer settings might also be worth looking at, but 3.2 supposedly doesn’t need those anymore...
Correct FFS version or other filesystem in the hard drive’s RDB?
I don’t have any direct experience with it, but a full system diagnostic with DiagROM could be worth trying. I wonder if it can be softkicked for easier use...