First thing we ever did in the tire shop I used to work at when something came in with a vibration problem was to check the inside of the wheels for mud buildup.
If that's ok, assuming the tires are ok and properly balanced, then your thoughts of a u-joint or as mentioned the carrier bearing are the next(and most likely) places to look. A miss in the engine that only shows up under load could possibly feel that way too. Try holding the brakes with it in gear and giving it gas(powerstalling the engine) and see if anything shows up there under load).
Turning the converter on the flywheel should not have any effect on balance, and in fact some of 'em will only go on one way.
You might also look at the pulleys on the front of the engine as it's idling to make sure none are bent or possibly the bottom pulley or fan/waterpump pulley did not get fully seated when they put it back together.
One final thought, if somebody else did the work, is that possibly they could ruined the balancer when the pulled it off and stuck one off a 400 back on there in it's place, although this would most likely be much more noticeable than what you're talking about.
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Today's Featured Article - Show Coverage: Godfrey, Illinois Country Days - by Cindy Ladage. Except for last fourth of July's Old Gold show in Springfield, Illinois, I don't remember when it was so hot. Nevertheless, the heat didn't keep vendors and visitors alike from enjoying the third annual Country Day's Event. Jane Elliott said the event was originally a one man show. "Barry Seiler, owner of Country Town Farm Supply store used to invite people up to the Johne Deere store. He would give hats and a free meal for everyone that brings a tractor." Elliott said while this
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