CV shaft is perrty forgiving but I would guess if you get out of the tolerance zone you will experance massive vibrations and pinnnion angle too high will mess with diff oil levels and splashablity or slingablity of the gear oil = HOT rearend
For mesurement without a shaft installed just point the pinnion at the xfer case and measure (cap center to cap center), when they make the shaft it will have in/out movemnt that will alow your mesurement some flexabilty, so it doesn't have to be a super perfect mesurement.
.02cents
