Denny,
The throbbing you mention sounds like you are observing a beat frequency, where you are getting a periodic aiding and cancelling of two or more separate vibrations. The run-out numbers don't seem to be excessive, but if they stacked up on one side, it would seem possible to get that condition. What happens if you accelerate slightly or decelerate when the throbbing occurs? Have you tried moving the tires/wheels front to rear? Have you measured drive shaft angles and checked the center support cushion and bearing? (I haven't read the entire thread, so I'm assuming a two-piece drive shaft from your description.)
I also note that these are all questions, and no answers to your situation.
Harvester
