I've had this problem and just had a professional fitting on my bike. We figured out that lowering the seat and moving it forward just a small bit made working on the proper pedal stroke easier. I'm trying it like this for a few rides and we may tweak the adjustments a little more after we see how it goes.

The first ride after making those tiny adjustments, meaning a centimeter or less, was amazing. I still have to concentrate on breaking my toe-down habit, but it's easier and feels more natural to do heels down with the adjustments we made.

If you have access to a professional fitting, I highly recommend it.