My assumption is that the marking of the drive shaft does indeed have to do with the orientation of the spinning with the relationship between the rear and the front being the same (how things line up). Before I took my drive shafts off in my driveshaft adventure experience, I did notice that when parked, all of the grease fitting (front and rear) were all the same--so basically even though the front is out of phase by 90 degrees and the rear is not, the zircs would be facing all the same direction (generally 'out') relative to the DS that they are on (they should all line up). For example, with the front DS out of phase by 90 degrees, I wasn't able to hit the one up front (on the yoke slip) because it's orientation was facing it up into the belly of the engine area. The rear one, was facing out and was accessible because it is in phase and was facing an available spot for me to hit with a grease gun. I then had to move back or forward to get the front one to appear in line so I could hit it with the grease gun (while the rear one went to a position that I could not reach--thus the 90 degree shift).
That said, I rebuilt my DS's which meant that even if I did put match marks, they were going to be gone after I replaced the flange going into the diff., along with the mark on the yoke slip as well as on the dust cover and u-joints.
And for balancing, they take the DS off the truck for balancing--ie: each shaft is balanced by itself, for itself...they don't balance the shafts on the truck (as far as I know with the experience I had at my DS shop).
I would say that the matchmarks are generally used in the FSM because rarely do people actually replace drive shafts. they are inspected, cleaned, and regreased. So, the matchmarks are (again, maybe) there to allow for the DS to be replaced right back on if things are ok with the DS after removal (so you don't mess with the original orientation).
I would try as hard as possible to 'remember,' or 'visualize' the orientation of the DS's before you took them off and try to get them back that way again.
That said, if you did do a lift and you are experiencing DS problems, maybe a rebuild might be a good option (or at least new u-joints then a balance).
DISCLAIMER: I am not a DS expert, but just relaying what I experienced and what seems to be intuitive to me at this point. Folks like Christo or Robbie, or CDan might have some better judgment on these issues.
If it's any consolation, I'm just running my front DS currently and won't have my rear DS for another week. I do not have match marks on the new rear DS when I get it. Just going to throw it on and hope for the best.
