Lincoln Motor Failure: OBD2 Codes P0345 and P0349 After Engine Replacement

Good afternoon, I'm experiencing a serious issue with my Lincoln vehicle. After replacing the engine, I started hearing a loud knocking noise that sounds similar to a diesel engine. The sound is particularly noticeable when the engine is under load or during acceleration. In some cases, the engine misfires and the check engine light activates, displaying OBD2 fault codes P0345 and P0349. I already replaced the gear actuator components on the crankshaft position system, but instead of improving the situation, the problem worsened. The engine now fails to run properly—four cylinders (5, 7, and 8) are not firing at all—which results in significantly reduced performance and increased engine vibration. The vehicle continues to trigger the same P0345 and P0349 codes despite these repairs. I'm seeking advice from anyone with experience dealing with similar issues on Lincoln engines. Could someone please share insights or potential solutions for this persistent problem?