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We see that the base is indeed > 5V, but collector and emitter of Q2 are both way above 3.3V. This indicates that the 3.3V zener has given up. After replacing the zener we have a proper signal when the test runs:
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Light blue is the signal on pin 6 E7, yellow is the signal on pin 4.
After this, and after messing with some floppies I got this:
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It looks like an entire pass tested OK 
During the test I could see the head moving; first track by track, after that reading random tracks… This part seems to be OK
Running the test with both drives filled with a properly filled floppy shows:
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