P0345 and P0349 Fault Codes on 2015+ Mustang GT After Engine Rebuild - Solutions & Diagnostics

I recently completed a full engine rebuild on my 2015+ Mustang GT, replacing the alternator, starter, relays, CPMS (Crankshaft Position Sensor Module) 2x, and battery. Despite replacing both the crankshaft position sensor (CKP) and camshaft position sensor (CMP), the vehicle continues to display persistent fault codes P0345 and P0349. The car now makes a loud rocking noise, struggles to start, stalls intermittently during startup or while in gear, and exhibits a rough idle. I've already cleaned all wire harnesses and the Powertrain Control Module (PCM), but the issue persists. The timing chain and phasers are confirmed to be in good condition. During my latest oil change, I discovered metal shavings in the engine oil—this is highly concerning. Given that these fault codes relate to sensor readings, could there be an underlying mechanical failure such as a damaged crankshaft or camshaft? Are there known issues with the 2015+ Mustang GT's sensor wiring or PCM calibration after major rebuilds? Any real-world solutions or diagnostic steps for P0345 and P0349 on this model?