Ok Here is the wiring diagram and the connector pin chart again, this time I blacked out the 5.9 stuff to avoid confusion. Wiring Diagrams for cummins has been known to be incorrect on the wire colors for many circuits. So we will have to do this by a process of elimination.
Wiring Diagram --->> Click Here to view <<---
Connector Pin Chart --->> Click Here to view <<---
Ok now on to the connections.
Pin 1 is going to be the Brown/Pink Wire
Pin 2 is going to be the Brown/Orange wire
The rest are going to need to be figured out by running some voltage tests using a multimeter with the key in the "Run" position.
One of those 3 wires is going to be the 12 volt supply. Whichever one that ends up being needs to be hooked up to cavity 6.
One of the two wires left is going to be the 5 volt supply, this is going to be hooked up to cavity 5. This should be the Pink/Yellow wire or as per your post Orange/Yellow.
The last wire is going to be hooked up to cavity 3.
Hopefully that will work but read below just in case..
You may find that these last two wires are both 5 volt circuits. at this time you may be able to figure out by looking at the wiring diagram for help with the colors, If that doesn't help, you have a 50/50 chance of getting those two right. Connect them to the remaining cavities and then try to start engine. If it runs, check for fault codes in the fan circuit. If no codes, you got it right, If codes present, swap the two wires and all should be ok...
Keep me posted and let me know if you have any additional questions...
let me know how it goes