Finally found out the final say on the drive shaft. It was in spec as far as the balance tolerance was concerned. However, upon re-balancing, they were able to get the shaft into much better tolerances.
The re-balance did help with some vibration. However, it does still have vibrations. I am confident it has to be coming from the rear axle gears/bearings. I did not have a dial indicator so i could not check out the backlash on the axle. But it did seem like there was an excessive amount. That paired with the notch-y feeling bearings have to be what is giving me my vibrations. I guess the search is on for a 14B SF.