I think you need a tune that illuminates the EGR which I believe is the majority of your problems. I personally like GDE tunes, but there are other tunes out there. If you don’t get a GDE tune make sure whatever tune you get turns off your EGR. My second suggestion would be to run Amsoil diesel...
I have a 2016, that I bought new. So far I have 45K miles on the truck with zero problems. I run Amsoil 5w40 diesel engine oil. I was BLESSED enough to get a GDE tune before the BIG BAD EPA shut them down. I plan to drive the truck until it dies.
I refuse to get it, I don’t want to give up my GDE tune, and I do not have a back up ECM to swap out for the update. The GDE tune electronically bypasses the EGR valve. I have been checking it and it shows no signs of leaking.
Well I guess we can still hope, without some type of hot tune these trucks are not the same. I got the EPA update from the dealer and the mileage was reduced drastically. Thank GOD I got my GDE hot tune before the EPA shut them down.