Did you check the ring gear for "run-out" when you did the install? I set up rear ends and I'm thinking something in the diff. Also, Woods builds different shafts for different uses, If you got one, say for crawling, it would be smaller diameter and thicker tubing and harder to balance. The one I installed on my 96' was built more for street and light trail use, thus having larger diameter and thiner tubing, easier to balance.
I'm not being critical just trying to find a solution.
You have a very similer set up to my 96'. Except the front is open and Tru-Trac in the rear(4.10 and 30"), and I'm running mixed bag OME/ACOS/TeraFlex 4.5" lift.