I had this same type of problem before, I got rid of most of it by changing the U-joints and correcting the pinion angle. I fear that the rest of the vibration is coming from a sloppy tranny slip yoke/internal bushing. I got a new trans and driveshaft coming soon, but it is 95% better by swapping the U-joints and adding some shims to the rear end.

Just because the U-joins seem ok doesn't mean they are. Drop the shaft and at least check to see if any rollers got out of place when the original install took place, mine seemed fine and there were at least 2 pieces of roller in the original caps.

Tom