At a glance, the two test dumps you just made look OK, so your setup seems to be working.
Your original dump contains the same couple of tracks over and over again. Since everything else seems to work, that indicates something caused the drive head to jam while reading the disk. It read track zero five time, then track one a bunch of times, eventually gets to track 2, then goes back to track 1, and eventually gets to track 3.
Unfortunately, the kryoflux log does not show this detail, but only indicates *HT where the "T" indicates a track ID mismatch. In the GUI the track mismatch error is obscured by the "H" informational message indicating sectors may have been written to after the disk was mastered or formatted. (From the tracks it did read, It looks like your disk was not professionally mastered, so the "H" informational message is irrelevant).
So, what you need to do is redump the disk while keeping a very close eye on the drive head to make sure it is stepping forward at each track.
Since the other disks dumped OK, my suspicion is something on the disk case or shutter that is intermittently coming in to contact with the head, and did not happen to cause problems on your Transcopy machine. There could be something jammed in your drive although it is not always causing problems. I doubt it is anything on the disk surface, as that almost always prevents the disk from even spinning in the first place. I've seen power issues cause problems with stepping, in those cases the drive will also sound weird, but powering down/checking cables/restarting usually fixes that.
Right. After reading your comments I decided to supply the power to my 3.5" floppy drive not via the adapter I got with my KF but via a PSU from a 486. I still get the "Error: Extra data was found hidden in unused paths on the block header", but I don't get it overlapping to track 83. The last three tracks are greyed out as per the norm with no data.
So...darn power issue in the end. At least we have the 3.5" versions archived now They are available on the usual places.
Thanks again for your help.