5) The trucks come from the factory setup with the Glow Plug system to be connected to the 24v side of the truck. This helps in a battlefield environment when jump starting the vehicle. The BIG resistor pack that is laying on the intake manifold allows the system to work.
Many people will remove that resistor pack as it helps avoid cooking the glowplugs. You will need to decide how you want to handle it. You options are reattaching the resistor pack to the wire wall or removing it.
If you decide to remove it, remove the wire from the 24v buss bar and the wire from the top post of the glow plug relay. Make you a jumper wire from 8ga wire and attach it to the 12v diamond shaped buss bar next to the relay and the other end to the glow plug relay.
6) You need to reattach the wires at the 24v buss bar. They are for the GEN2 alternator.
7) Where does the blue wire go? Does it go to the starter? It is not factory.
8 ) Post a picture of your battery cables. If you have a picture with the batteries installed, please post it so we can see if they are hooked up correctly.
9) Have you checked the starter relay under dash? You may want to do the Doghead Relay upgrade.