Your axle assemblies are clocked and balanced as an assembly. If you disturbed the clocking between segments or bearings, then you most likely have caused the source of the vibration.

To correct this, you must disassemble "the CV joint" you had apart when you messed with bearings, and turn either shaft end 120 degrees, and reinstall in that position and test drive.

The good news is you only have three ways to screw it up, provided you didn't take the bearing yoke off the main shaft or anything. If you had the yoke off the shaft, then the number of possible errors are equal to the number of splines on the shaft times the number of yoke bearings. If this is the case, good luck. If you only separated the main joint, then it should be easy to fix.

Let us know how you did.