Cat 3406e getting hot

How are the other temperatures: oil and pyro?

 

I have no direct answer to your question but will say this. When I have been in situations similar to that it is best to clear my mind. Forget I know anything about this truck and start from scratch.
Bottle test? Coolant pressure in block? Temperatures at the top and bottom of radiator type things. Infrared heat guns are great.
You have a great amount of knowledge at your fingertips. Those guys have and others will give you great information. I just suggest a new start. A shop rag in the system is not in the troubleshooting flowchart.
Are the air to air and condenser clear?

 

Test charge air cooler for a leak,

 

If the problem persists after all the possible causes you have addressed with parts and labor, what remains common from before the overhaul to now? I had a problem with the electric temp gauge in my 93 w9. It would have temperature flare ups similar to yours when the marker lights were turned on. The electrical issue magnified the normal rises in temp even though engine was not getting hot enough to trip fan switch on. Probably a grounding issue... changed to oem mechanical temp gauge. Problem solved
Also,.... when the engine is heat soaked from normal to heavy use your oil temp should exceed your coolant temp by 15 to 20 F. That is with it reading from bottom of oil pan. If taken from oil cooler directly it doesn't have to be a heat soaked to show that. After all, oil cooler is water cooled and is not 100% efficient.

 

My W9 is full mechanical so there are really only one set of senders monitoring temps that I can see. Our 379 C15 has (and I am no authority on the way this is all set up) sending unit in bottom of pan for oil temp gauge and a separate sender that the ecm monitors. Water temp, same deal, different locations. I have replaced everything for the coolant gauge. Wiring, gauge, updated wiring harness weatherpak, ground, supply voltage... and it does about exactly what yours is. After it gets warmed up it is likely to be reading 230 to 240 idling a bit or driving normal down the road. No cel. No alarm. No debate. Take and have ecm history of events and no record of abnormal temps. Finally bought a Scangauge. It reads what the ecm is reading in real time. Oil temp, psi, coolant temp, fuel temp, intake air temp, horsepower and mpg as ecm calculates it. You can tweak mpg readings with real pencil figured data, however, I never have and my readings are more accurate than I would have ever believed. Under 200bucks shipped. 5min install and quick setup. No more ulcers from temp gauge. Check you ecm history.

 

One more thing while I am rattling. Get infrared gun and take readings at sender locations and compare. Get someone to go with you to get hood up quick after a pull and check around stat housing for peak temp. That was 1st clue on 379. Gauge at 220. Infared at 195.