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[Chamberpains]

100% this could be the root of all your problems. Being that you have replaced almost everything under the hood and we're going to assume they were replaced properly. I would definitely start out looking at the tune that is in your ECM. But this is after I would verify that your gauges are correct. There's no sense in getting excited if it's actually just gauges.
Do you know how to get your current calibration # and cpl # out of the ECM? You can get the cal # with Cummins Insite and the CPL# off the data plate on the valve cover. And also do you know how to look up what the original calibration# and cpl# was supposed to be in your ECM? Which can be looked up on Cummins website or the free android app Quick Serve and using your engine serial number. Hopefully you have the original number off the original engine in your truck. My long block got replaced with everything new from the valve cover down including the engine data plate. Now the serial number starts with 8LB00xxxx (LB for Long Block) and is completely unrecognized on quick serve. If you don't have the original engines serial number you can get that from your truck manufacturer. Just call any dealership and ask them for the original engine serial number.
With those numbers we can use that as good starting point to see if you have at least the start of an acceptable calibration in your truck.