Good news! I've managed to have it booting! 
So it actually turns out my external hard drive was on its death bed, I used it for a few minutes with my Power Macintosh 8500 and it just died with horrible noises. It's understandable though, it was a 20 MB CMS drive from the end of the 80s...
I've replaced it with the 4.5GB hard drive that was sitting in my IIsi, which has been organized into three partitions: System 6.0.8, 7.1, 7.5.
I had to fiddle with it for a while because for some strange reason it wouldn't change its SCSI ID from 0 even when configuring the jumpers; in the end I just left it with SCSI ID 0 and I changed the Miniscribe to have SCSI ID 2. And behold, the SE just booted fine with 6.0.8!
System 6 complained that the Miniscribe was unreadable, so I just initialized it. I tried putting the system folder in it to see if it could boot from there, but subsequent tries to boot from the internal hard drive have resulted into multiple "Illegal instruction" bombs, while nothing wrong happens when booting from the external hard drive. I guess it must be dying, too?
In the end I just disconnected both the Miniscribe and the floppy drive, which was making very terrible noises as if it was going to explode!
I hope it's still salvageable, but if it's not I'll probably look for another superdrive from an LC or similar devices, provided they are compatible.
I'm also going to replace the Miniscribe with some other SCSI drive - any particular advice regarding the maximum capacity I shouldn't cross, or power consumption limits? I know System 6 can't read partitions greater than 2GB in size and pre-68040 systems cannot use volumes larger than 4GB, but other than that I don't know if there are other limitations. Ideally I would want to avoid taxing the power supply too much.
Speaking of power supplies, I'll see to have it recapped by Ferrix as soon as I can: it's mostly working now, but I noticed a couple of random hangs earlier and some very strange things happening with portions of text replaced by garbage content. I'm sure it's not bad RAM or corrupted files because they've both been in full usage with my IIsi for a long time and they've never shown any sign of instability, so I'd say it's just as tech said: the 5V rail gets too weak and causes bus glitches, freezes and so on.
I've also noticed that the CRT has some burn in, but overall it's still very acceptable - you can see it when it's powered off if you look carefully, but with the system running is effectively unnoticeable.
So it actually turns out my external hard drive was on its death bed, I used it for a few minutes with my Power Macintosh 8500 and it just died with horrible noises. It's understandable though, it was a 20 MB CMS drive from the end of the 80s...
I've replaced it with the 4.5GB hard drive that was sitting in my IIsi, which has been organized into three partitions: System 6.0.8, 7.1, 7.5.
I had to fiddle with it for a while because for some strange reason it wouldn't change its SCSI ID from 0 even when configuring the jumpers; in the end I just left it with SCSI ID 0 and I changed the Miniscribe to have SCSI ID 2. And behold, the SE just booted fine with 6.0.8!
System 6 complained that the Miniscribe was unreadable, so I just initialized it. I tried putting the system folder in it to see if it could boot from there, but subsequent tries to boot from the internal hard drive have resulted into multiple "Illegal instruction" bombs, while nothing wrong happens when booting from the external hard drive. I guess it must be dying, too?
In the end I just disconnected both the Miniscribe and the floppy drive, which was making very terrible noises as if it was going to explode!
I hope it's still salvageable, but if it's not I'll probably look for another superdrive from an LC or similar devices, provided they are compatible.
I'm also going to replace the Miniscribe with some other SCSI drive - any particular advice regarding the maximum capacity I shouldn't cross, or power consumption limits? I know System 6 can't read partitions greater than 2GB in size and pre-68040 systems cannot use volumes larger than 4GB, but other than that I don't know if there are other limitations. Ideally I would want to avoid taxing the power supply too much.
Speaking of power supplies, I'll see to have it recapped by Ferrix as soon as I can: it's mostly working now, but I noticed a couple of random hangs earlier and some very strange things happening with portions of text replaced by garbage content. I'm sure it's not bad RAM or corrupted files because they've both been in full usage with my IIsi for a long time and they've never shown any sign of instability, so I'd say it's just as tech said: the 5V rail gets too weak and causes bus glitches, freezes and so on.
I've also noticed that the CRT has some burn in, but overall it's still very acceptable - you can see it when it's powered off if you look carefully, but with the system running is effectively unnoticeable.