Different models of vehicles may have the same fuse box and the fuse box cane be labeled the same way. However, the wiring harnesses may be different colors based on different accessories in that vehicle. The color of the wires not matching up statement I made was because of this. Your truck may have a standard stereo system where as the truck that you got the fuse box from may have had a premium sound system and included wires in it for a amplifier. Because of this the color codes may not match up. I believe diesel vehicles have a different wiring harness also. Wire color is not that important.
You need to make sure of each wire coming out of your truck goes to the correct slot on the fuse box. For example, the wire that you know for a fact is coming from your cigarette lighter circuit is connected to the fuse slot labeled as "Cigarette lighter" on your fuse box. Even if the wire colors don't match.
The circuit going to the headlight circuit must be connected to the "headlights" circuit on the fuse box, regardless of wire colors.
I guess the first thing I should have had you do is this. Before disconnecting anything on your original fuse box is to photograph it for later reference. Then compare the new fuse box with the original one. First, is the fuse box the same shape and dimensions as the original. Second, do all of the slots in your original fuse box that have circuits in them ( the slots that have the metal connectors in them ) match up with the replacement fuse box. Sometimes the plastic housing will be the same but the circuits being used may not be the same. If all of the same slots in the fuse boxes are being used on both fuse boxes, then you can compare wire colors to see if they are the same colors. So, for example, if both fuse boxes have a circuit going to the stereo and both wires coming out of each fuse box are a blue wire with a white stripe, then you would connect the same color wires when you swapped them over. But if the colors were different between the fuse boxes, then you would make sure the wire coming from your truck goes to the new fuse box connector that is labeled "Radio". The color wouldn't matter in this case, just the wire gauge.
As far as your hazard light issue, I cant figure that one out. I probably would need to see it in person to make any conclusions on that one.