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SE FDHD Internal HDD won't boot

I found this little beauty in a dumpster years ago and managed to get it running System 6 just fine. A few years (and a few moves) later I tried to turn her on and all I get is the question mark floppy. I booted from an install disk and ran the disk utility for system 6 and it wouldn't recognize the drive. Originally it had a 40mb apple drive in it that I tried replacing with two different 20mb drives. Still nothing. I replaced the SCSI ribbon even. Still the disk utility won't see the internal drive. I can boot it from an external SCSI drive no problem. Clearly that original internal drive is fried but why won't the others work? I can only assume it's a problem with termination or jumper settings or some other aspect of old SCSI drives I don't know a thing about. Is it possible that just the internal scsi has died. Is that possible without affecting the external SCSI? If anyone can offer some explanation I'd appreciate it.

 
Try another disk formatting utility like HWB, or others. Apple's drive formatting software from that era will only see their OEM drives without a hack.

 
Originally it had a 40mb apple drive in it that I tried replacing with two different 20mb drives. Still nothing. I replaced the SCSI ribbon even. Still the disk utility won't see the internal drive. I can boot it from an external SCSI drive no problem. Clearly that original internal drive is fried but why won't the others work? I can only assume it's a problem with termination or jumper settings or some other aspect of old SCSI drives I don't know a thing about. Is it possible that just the internal scsi has died. Is that possible without affecting the external SCSI? If anyone can offer some explanation I'd appreciate it.
Do you hear the drives spinning up? Many drives of that era and vintage suffered from stiction (Sony 20MB drives were notoriously unreliable, as were certain Quantum 40MB drives). Also, make sure that the drive jumpers are configured properly, and that the termination resistor packs are in place.

 
They do spin up. The drive access light blinks when it tries to boot. The termination packs are in place. Also, i have no idea how to set the jumpers on these old drives. Are there any guides for that?

 
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