Try unhooking the aftermarket harness from the factory harness and see what the drain is, perhaps something in the aftermarket harness or radio is bleeding voltage into someplace it shouldn't.
Always been your truck? If not, look for any thing that probably shouldn't be there, under dash electronics wise.
A wiring diagram can be your friend here, if nothing else as a way to explain everything attached to the fuse(s) you pull to stop the drain.