The read/write data pins on a floppy drive do not correspond to flux-value (e.g. 1 for North, 0 for South). Instead these signals supply a falling-edge at each flux transition... and the duration of the low pulse is somewhat arbitrary. Thus, I don't think it's possible to know the polarity on the disk. Though that doesn't matter. What does matter is that we can't just drive the /WD pin with our PWM signal, as will be stored on the media...