So what is that deep knocking sound coming from the motor? just about every oil burner I've ever stood next to has this same knock. It's th loudest when your head is right in front of either door. Any help on this one? and no it's definately not rockers or pushtubes

 

You think it might be the compression knock/power knock the diesel engine makes? This is just my thoughts on what your hearing without hearing it myself. Since diesels ignite the fuel with compression they make a rather knocking noise.

 

It's definately not any type of ignition noise. It sounds like a rod to me. Almost every cummins I've stood next to has this noise

 

My ole trucks both have a compression knock. Do you have an automatic? Your sig says you do but maybe you have upgraded to a manual. It might be the flex plate having a crack in it knocking, i've seen this and heard a knocking noise that sounded like a rod knock. But without hearing what your hearing I don't know. Maybe for grins and to be sure, if you do have an auto, check the torque convertor bolts and the flex plate. Good luck with it.
ps. I looked at your pics--where did you get your gauge pod on your dash?