Just reading through, just trying to respond on the situation on knocking and alignment. I've only had it happen once I can remember.
So there is a routine in the BIOS that calibrates the drive by moving the head all the way out (towards back of drive) looking for the track zero switch. There is a black screw on the back that prevents the head from going too far.
IMD also does the calibration seeking when you tell it to use the drive. If you are saying that you heard some knocking when starting up IMD or the PC, then I'd check:
1) is the track zero switch working as expected -- you can check this in IMD.
2) you can check the alignment screw for track 0 -- this is part of the alignment check
2b) you could try to step even further backwards beyond track 0 -- this should not be possible
I had this happen too once, when I cleaned one of these drives, and then started it up again. I don't know for sure, but I'd suspect that it was the alignment screw.
So I aligned my drives without an alignment disk in IMD. It's totally doable. I did figure out how to use an oscilloscope to see the signals mentioned in the tandon manual. Not sure if that really helped, but it might be possible when fine tuning is needed.
I do totally agree that you should make sure the floppy is in good shape, when you are testing the drive.