Hi. Thanks for using JA! Sorry for the delay.
It sounds like you have done alot of good work so far. I know that situations like this can be very aggravating.
Since the air system from the turbo to the air to air core is good and I assume that your engine has good fuel pressure (65 tp 90 psi). There are 3 things that come to mind about your problem.
The first is the accuracy of the temperature and pressure sensors. I know that you have already replaced the atmospheric sensor, but whenever I have problem like this, I like to verify that the Boost, Intake Air temperature, fuel temperature, and atmospheric sensors are reporting accuractly when the problem is occuring on the engine. In order to do this, someone will need to have ET hooked to your engine while the porblem is occurring. I have seen sensors read way off causing the engine to have problems.
The next thing is an injector harness. I know that you have had some of the injectors replaced and well as the ECM, but I have seen the injector wiring harnesses under the valve cover cause a miss under load with no fault code.
And lastly, is the fuel supply and return lines to the engine. If they are restricted, it could cause the engine to miss. Also, problems with these lines will not show up on a DYNO because these lines are bypassed. Unless the operator runs the truck with the lines hooked up normally and not to the computer.
When your truck was run on the Dyno, did the problem happen?