A friend of mine wanted to see the motor yesterday, and I was showing him some things. I noticed that Cummins/Dodge put a ton of alignment marks on the electrical and fuel connections as well as spraying a clear coat? all over everything.

I am thinking that there are using this as a "tell" to know if the harnesses have been undone/redone (box) or if the fuel system has been messed with. I remember a few of these on my 04.5, but the marks are everywhere on the '06.

Maybe it's just QC at Cummins to make sure everything was installed and checked?

 

I think you're right.
If you look under the truck, you'll most likely see similar markings around fill plugs and important bolts as well.
Greg