One way to check for shorts is to disconnect the negative cables from your batteries and then rig a test light between the cable and battery post. You'll only need to do this on one battery. Then you pull one fuse at a time until the light goes out. This'll give you the circuit that is giving you the problem. Hood lights and open doors will fool you because the lights will complete the circuit so pull the bulbs ahead of time. Once you have the problem circuit you can get a wiring diagram and start chasing the problem. Usually it will be in the one circuit that powers most of the truck. Have fun, I've spent some serious hours doing this over the years.