Axle and flex joint ballance?

[kaoskingnd]

Well had the flex joint changed on the 90-300sel. It was pretty easy but, the mechanic forgot to mark the front half of the drive shaft and now there is a harmonic vibration at all speeds.
The rubber on the center bearing is pretty bad but the bearing was fine. Is it possible that being off by a few splines can throw off the ballace that bad?
It was not there before.
I also need inner and outer tire rod ends. Have them on order.
Is there any marks on the drive shaft that will aid in the proper alighnment and ballace?