I strongly doubt it's the spider or side gears. These see relative motion only when you're turning. and even then the rotation rate is so small (dictated by the difference in speed of the road wheels) that wear is practically unheard-of.
When do you hear the clunk? Under what conditions, specifically, do you hear noise? Turning? Accelerating? Decelerating? Just starting? Just stopping? Transition from drive to coast?
If you are intent on going to 3.73s then the ring and pinion are going to be swapped anyway and you'd be wise to invest in a kit of parts that includes all new bearings and races. As long as the rear hasn't been run dry the side and spider gears should be fine.
But you should make sure that the clunk you're hearing is not related to the
control arms, bushings or even the mounting points on the chassis and floor behind the rear seats...