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Was anything done with the timing or did you install the engine as is/was?Did you use any parts from your original engine?
Since the car is giving timing codes (both cam sensor codes) and one variable intake code, I find it most likely the noise is from the timing chain, most likely the metal they are finding is from the chain as well.
Clearly something is causing the timing to be off on the car which is why it's setting cam sensor codes for both sides of the engine. I think new timing chain tensioners and checking the engine oil pressure after running for a bit would be the best place to start with this. I assume they are saying the oil pressure gauge on the dash is staying normal. What they really need to do is check the actual oil pressure with an oil pressure tester at the port for the sending unit and not assume the gauge on the dash is accurate.
I would seriously be looking at timing components as the problem here.
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