Using Interrupt On Change you'll get an interrupt every 3.33mS. I think all you need to do is check the pin number and polarity of the interrupt (rising/falling) for the sequence and reset a timer set to overflow at ~3.5mS. If the timer overflows, you're missing a phase.
Of course, you already know you can connect the phases through current limiting resistors as shown in Microchip's AN236.
If you output A, B, or C for a rising edges and a, b or c for falling edges you should see ABCabcABCabc...
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