Did this problem gradually appear or suddenly appear? I would check things like your motor and tranny mounts. If they are screwed up, your motor could be slightly of of line and putting a little pressure on the shaft. The shaft is designed with an inner "plunge" joint. As it tries to plunge inward the motor is not letting it, creating a vibration. This type of problem would have gradually appeared (usually) and would still exist although the axle was changed. This is the only thing I can think of outside of something being bent or maybe a bad hub bearing. Good luck.
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