99% of the time the carter pin comes out of the hole holding one of the rods. And thats why one side still works and the other side doesn't.
Fixing it is not a "hard" job, but does require patients.
Remove the 2 bolts on each side of the tailgate hinge and then take the tail gate off. When putting the tail gate back on the alignment is done by adjusting the hinge plates up or down to square the tailgate in the opening and make sure it is the proper distance from the top hatch for a good seal.
You'll need to remove the tailgate. Carefully remove the latch, remove the one rod thats still attached and secure it w/ a long piece is wire, so you can pull it back up to the hole when you're ready.. Then fish the other rod up to the hole where you can see it. Reinstalled both rods w/ new carter pins, and then put the latch back together. The latch has to have some spring-tension by way of jamming a shim in the striker to allow you connect the rods. The correct orientation of the latch can be tricky, often times its a trial-n-error process to get it to work properly and fully retract.
If the bolt is rounded off, you'll need one of these
http://www.wildhorses4x4.com/product/Tailgate_Handle_Pivot_Bolt
Often times when the tail gate is off this is a good time to get rid of one more rattle by using new bushings for the hinge.
http://www.wildhorses4x4.com/product/The_Silencer_Tailgate_Hinges
