confirmed that there are two index tracks, one at track -2 (relative to user data starting on track 0) and another on track 616 (user data ending on track 614). the D2 square wave is directly from the hall effect sensor, 2 cycles per revolution. the D1 pulses are this signal divided by 2. MCU read data is the index signal as seen by the MCU after being processed with a one-shot.
here is a closeup. the raw MFM data shows a square wave of 5MHz for most of it, but there is a short section (4ms long) of 1.8MHz. the one-shot acts as a primitive data separator and the MCU can then detect this index marker and reset the hall effect divider flip flop.