I have been following this. You say all you changed was the rotor and the problem appeared, so I would think it's not the feeder. Rumble is a sign of the material staying in the rotor area too long. Have you checked the condition of the vanes in the cage and cone, if they are worn and the rotor being new it could cause what you describe. The Harvest rotor has all straight rasp bars on it in a helical pattern yes, but it will rumble more when it gets tough than an afx/or specialty rotor.
Straight bars were added to a specialty rotor to keep the material in the rotor longer, each set of bars would add 1-1.5 revolutions to the crop in the rotor and two sets can be installed. The Harvest rotor will keep the material in the machine longer as it is all straight bars and in tough-damp conditions it will show.
I think the Harvest rotor was developed in western Canada and the conditions are dry (low humidity) and not too many green stem soys grown there either.
If you install a set of disrupters in the grate area it help your problem. Your into it for $5000.00 so what is another $500.00.