JAshpaugh,
I have a 2004 (not 04. 5) Quad Cab CTD with a 16K superglide and the super rail system. For my truck, it's not exactly a rail, but a set of 4 brackets which mount to the frame. The only thing which comes up through the bed is the four mounting posts for the hitch cross-rails. I just installed a set of Firestone airbags and they went on in under two hours. They may be the easiest set of aftermarket items I ever installed.
The bags rest on the axle inboard of the springs and then replace the jounce bumper above with the bag mount. The Superglide brackets are cut out in such a way as to allow both items to fit with no interference. I couldn't believe it. The Superglide folks must have thought of it, because it just can't be a coincidence that they fit so well together.
Is this the setup you are talking about, or are you trying to do something a bit differenct?