Are your u-joints in good condition? Have you looked under the car when the driveshaft is spinning and is there any obvious signs of the driveshaft being bent?
Hmm good question! How would I recognize a bad U-joint? When I replaced the transmission, the U-joint seemed fine...as in bearing were smooth, nothing too pitted.
As for obvious bending of the driveshaft...I didn't notice any, but I'll take a closer look next time I fire it up. That's a great idea..and I don't know why I didn't think of looking at it while it was spinning!