My old tailgate was very rusty and the window stopped going up and down due to one of the window guide brackets rusting out and throwing the window out of alignment and a rusted regulator.  Rather than try to fix it and worrying about how much longer it would last, I decided to replace the tailgate shell with one from CertiFit for $190.  I have listed the steps and tips from memory so I may have forgotten a few  things.  The whole job took me a weekend to do.

This is what the outside of my old tailgate looked like.  The bottom edge was almost totally rusted away and there was some pretty bad surface rust on the top edge.

This is the interior access panel.  The bottom edge of the panel was rusted away leaving nothing for the screws to hold onto and letting it rattle around.

The first thing to do is to remove the access panel to allow access to all the tailgate internals.

Then you have to remove the screw holding down the access panel support on the left side of the tailgate.

Next, close the latch on the driver's side to allow the   window to move while the tailgate is down.  I moved the glass until it was halfway out.  Make sure the glass is supported- I used an adjustable stand that was originally used as a table saw extension stand.

Then remove the nuts on the two brackets holding the glass to the regulator.  Mine were rusted and two broke off.  The weatherstrips on my tailgate was rotted away so I could pull the glass out without removing the brackets from the glass.  If your weatherstrips are still in good shape, you may have to remove the rivets from the brackets to be able to slide the glass out or remove the weatherstrips.  Don't forget to unplug the defrost wires from the glass.