If the driveshaft was taken apart at the spline in the process without marking its relationship and reassembling it by aligning the marks, the driveshaft could be out of balance. If that were the case I would think it would be at all speeds, but it might cause what you describe.
Note that it is not necessary to completely disassemble the driveshaft at the spline to accomplish replacement of the flex disk, but it is very possible that it happened.
Otherwise, you need to see that the center carrier bearing is in good shape and the bolts are tight. Also wiggle the u-joint while you're there. Check everything driveshaft related since the vibration started at that point.