The truck is an '89 Xtra Cab with the 3vze, 5 speed, and stock 4:10s.

In the last six months, I have replaced the clutch and all associated components..

For the last couple of months, whenever I go from nonmoving to reverse, the truck hesitates for half a second, then something underneath makes a loud clanking noise. Right after the noise, the truck moves in reverse like normal..

This clanking/hesitation only seldomly happens, nor does it happen more while the truck is warmed up or still cold. The FSM doesn't point in any direction, unless I managed to reinstall the rear driveshafts without properly aligning the four bolts, but I don't believe that problem would only produce evident problems in reverse..

Any ideas?

 

Bad u joints.

 

I agree bad u joint,but where you have an extended cab you probably have 2 piece driveshaft, so you might also have a bad steady (support) bearing.

 

Most likely, you can slide underneath, and if you can turn the driveshaft more 10 degrees, or push the driveshaft sideways more than 1/4", something's wrong. Just find the place where there is slack (most like one or more u-joints, but it could be the support bearing).