31s won't do anything negative to your truck. You gotta pull the third and inspect it. Rear comes out easy enough. When you get it out look at the gears if there is any rea obvious wear on them they may be beyond saving. You should be able to see the play with the third out and ID the offending part easy enough, and a new bearing set should be in order. If you live anywhere near AZ I would have Zuk dig into them for ya.

(aka suprathepeg, aka Sean)
89 v6 SWB truck "BLACK BEAUTY" EB valves, P&P head 30 over.
95 FZJ80. Lifted. locked and rollin on 33s (my dream machine)