Replacing the u-joints will not affect the rig of the aircraft. The yokes may just stick out of the panel about a quarter of an inch further. At worst the yokes may not be perfectly level when the control surfaces are neutral or the yokes may not be level in relation to each other if your marking and drilling is a bit off. The nearest place to actually influence the adjustment of the rigging is several turnbuckles and limit bolts on the chain/cable driven by the yoke shafts.
Best of luck. Greg
