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(thinks out lound..)
If you could force different speeds and different voltages, you can make some guesses as to what the cable might support.
USB packets use CRC checks, so a bad checksum may indicate a speed or physical problem. (Besides stating the obvious, my point is that doing strict checks for each USB mode gives CRC more value.)
I just looked over the source code for libusb (like I knew what I was looking for, or something) and it seems that some of the driver(?) components hook really deep into the kernel. There might be a way to test specific parts of any type of handshake (for dataflow or voltage negotiation) to isolate specific wires that are bad by the process of elimination.
I think my point is that a top-down approach is likely possible, but it's probabilistic.