That clicking noise is likely just the solenoid on the starter. If so, you simply are not getting enough amps to the starter. IF your batteries are good (a single should start a 12 valve cummins all day) . I would first inspect the cables at the batteries, make sure there is no corrosion on or IN them (look for green/white powder inside the wires, (you may need to even skin a little insulation off the wire to see). Then check the ground side, and make sure your grounds are good and clean. Do the same with the Positive side, and at the connection at the starter. (bigger cables the better).
A little trick that will help- try to jump it with another car or another battery. Hook the cables DIRECTLY to your starter. (ground the ground of course). Put the positive directly onto the positive cable on your starter, (Starter, not solenoid) . This will get more amps to the starter.
A 5.9 should start no problem in 12 degrees, I run all the time and in way colder weather. You should have a Heat-block in the intake system. It is usually activated by a push button. This will warm the air going into the engine, and help it start. Another trick is to put a heat gun or a hairdryer blowing into the air intake to do the same thing.