Actually the recall was on 96-98 4Runners and updated the rear suspension to the newer 99-02 type, so that wouldn't affect him.

The Bilstein shocks are supposed to have a lifetime warranty , but I don't think shocks would cause this. What I would do is jack the truck up and put it on jack stands. Grab each and every one of your links on your suspension (2 upper, 2 lower, 1 panhard bar) and also your sway bar and endlinks. Basically, just check everything for play. Check the shocks too. Maybe unbolt them from the lower mount and try to compress them and see if they are equally pressurized.