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I see everything you have replaced so far, but don't see any components associated with the HPO system. Have you checked the ICP sensor and wire pigtail. ICP failure is common on the early models where it was located under the turbo and subject to high heat. I have had two sensors fail so far. I now carry an extra in the glove box. Late 04 builds relocated the ICP to the right valve cover. You can unplug the ICP which will make the computer go to the default setting for high pressure oil, and your issues may disappear. Doesn't hurt to try. My ICP failures made the truck run like it was "missing".
Pull out the IPR and check the screen for blockage or damage. A blocked screen will prevent the valve from properly regulating the oil pressure to the injectors. I had this issue as well. Have you air pressure tested the HPOP and listened for leaks? I recently completed work on an 04 that lacked power and had intermittent shuddering. The issue was solved by replacing the failing D ring on top of the HPOP which seals inside the cover to maintain pressure to the ICP and IPR.
As you probable already know, recheck the FICM connections, injector connectors, and FICM voltages for main power and logical power.
Overall, not too time consuming, and no additional money spent "throwing parts" at the unknown.