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1, Yes, the log confirms that the drive does not seek, or the track0 signal is not working.
2, Are you talking about real professionally duplicated originals or disks created by yourself?
For duplicated originals the only preservation I could recommend is to generate stream files for later analysation.
For user generated disks D64 is fine.
Note; the only way the KF would generate different D64 files at all is if it can sometimes read more or less data compared to other attempts.
CBM's drive firmware and most transfer programs that depend on that tend to replace illegal GCR nybbles with FF. Eventually they just match the very weak xor based checksum.
KryoFlux's host software does not work that way.
It verifies each and every nybble individually to be a legible GCR code and if it is not, even if the checksum is ok, the sector is marked bad - which is the right approach given how weak the checksum is.
I'll post a bit later about how to get the best read out of the disk.
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