1997 Ford F-150 vibration

I have a vibration in the rearend I think. When I opened the dif to change the fluid I noticed the spider gears were tore up in the limited slip carrier. I found a open rear for the truck with the same gears and installed it. I had the vibration before I changed rears. The clutches also spun in the carrier. The rear that I installed had a little movement in the pinnion flange, I tightened it up just enough to stop the movement. Would the spider gears and spun clutches in the carrier make that vibration? Also when the trans shifts(4r70w)either down to 1st or up to 5th there is a pretty good vibration and clunck. All other gears seem to shift perfectly. Thanks for your help, good luck.