Was the shaft lengthened for the new box (it usually needs to be)? If not, do that:
- http://www.4crawler.com/4x4/ForSale/Docs/BodyLift_HowTo.shtml#RecirculatingBall

Your clue that this is an issue is if the rubber rag joint is not sitting flat. Otherwise, the angle on the shaft may have changed enough that you need to re-align the plate where the shaft passes through the firewall. Mine has 3 bolts on it.