I have the stock unit.
A stock shaft has rzeppa CV joints and it really doesn't matter how they sit in relationship to each other. If you just lifted your Jeep, your output shaft and pinion will be parallel to each other and that's fine. If you have a 2-door and 3" of lift or more, I would save up for a new u-joint style shaft and upper rear control arms to set your pinion angle as it won't be long until the joints fail.