when my bearing started going bad, at first the noise would only show up after it got warmed up. it was there on accel and decel, and turning to one side or the other would lessen it/make it worse.

is it likely that the bearing just happened to start making noise after the diff/axle swap? not really, but it's possible. and yeah, if you wait too long to do the axle nut re-torque the bearings wheel definitely be ruined.

 

Only problem is that nothing in the rear end is factory anymore. The axles a brand new Driveshaft shop axles with r200 rear end.

Chris, any other recomendations on what the clicking might be? We are going to be replacing the rear brakes wheel bearing and axle nuts this weekend to see if any of this helps.