CoryM,
I had a similiar problem. Mine went away after replacing the tank selector switch. Check the connection on the tank selector valve. Sometimes moister can cause the connections to rust. If you want to keep the dual tanks try changing the selector switch. They are really cheap. <$12.00. With the ignition switch on, depress the tanke selector valve and check to see if you can hear the valve try to change over. If it does not then check the wiring and connection on the valve. If you hear it try to switch go ahead and replace the switch in the cab. It may be not getting enough current.
If you are going to remove and move the fuel lines be sure to move both the supply and return lines for each tank. Or you could end up using one tank and filling the other. Best option would be to completely removed the unused tank. Saves weights, no fumes or rust buildup and less mechanical stuff to worry about.
I would keep the dual tank selection. I like it because I don't have to fill up for almost three weeks with both tanks full. A cruising range of 500+ miles is also a plus.
------------------
Gerardo
1983 Custom Truck
TX Plates: "BAD BOW"
http://www.geocities.com/abetterchemist/