I found the problem today. The lower silent shaft rear bearing is shot:

I think I figured out why. When I had the engine rebuilt, I cleaned all the parts that the rebuilder did not get. The 2 front covers were some of the parts I cleaned. When I put together the counter-rotating gears, I must have not timed them correctly. I compared the shaft to the timing gear with a spare front lower cover, and the two shafts are not in the same spot. That probably caused so much vibration, that it took out the silent shaft rear bearing. I may have to pull the engine again, bummer....