How do you know for sure it is the drive shaft? what is your evidence?
What kind of vibration and when does it occur, is it constant, rythmic, random, more evident in turns ....?
I doubt it is the drive shaft unless you did some damage to it. Get it balanced and installed correctly. It should cost less than $100.
The body lift and shackles are my prime suspects.
Whenever a vehicle is lifted via a body lift you need to expect some additional vibration, especially in our vehicles. After all they are only a box on wheels and the aerodynamics are pretty bad. You my be feeling additional wind vibrations is all, you added more surface area which means more wind resistance.
When you did the body lift (3" is quite a bit of body lift) did you also replace the body bushings? If you did not put new poly body bushings on then I suspect this is the source of some vibration. The original rubber bushings, now 6 years old, are too soft to properly support a 3" body lift.
You didn't lengthen the drive shaft distance or change the angle enough with a shackle lift to cause the slip yoke to be extended far enough to cause a vibration. However, you could inspect it for abnormal wear pattern to confirm it. Also, try packing it with grease to see if that gets rid of the vibration.
Also as jobunn mentioned the shaft needs to be replaced in the exact same postion / orientation that it cam out. Ford had a TSR about this at one time. It basically stated that if the drive shaft was not oriented the same way as it was from the factory that there woulkd be a vibration, and there was no reasonable way for the shop to fix it.
Just how much longer are the shackles, and what type? These could be the culpret if they are simply twin bar extended shackles. For every additiojnal inch of shackle distance you only get .5" of lift. If you used shakles that are 4" longer than the standard to get 2" of lift then I would be very suspect of these. They should probably be boxed to give them additional strength to resist side to side motion (vibration).
