Good idea on the alternator. It doesn't sound like a bad alternator but at this point it's all a mystery.
What Itd02 said about the plastic timing guides is right they are easily breakable. Ive seen other motors plastic guides just as bad probably worse.
But even as bad as mine were there was only an occasional rattle at start up, no weird sound like this. And it was a motor with poor oil flow, surprisingly the adjuster seemed in decent working shape, but when those adjusters (like in my f150's 5.4) don't work there is all kinds or rattling and banging. (Btw the ford designed guides and tensioners are rubbish, every guide was broken and they are very long, the 3.7 has a much better design imho + a more stable timing setup.)
Oh, the weird sound I did have was a heater shield like rattling sound. Thought it went away with motor swap , it sort of did, but I found the power steering lines we bumping on the frame occasionally, don't know what held them originally so for now they are zip tied with a something soft insulating it so the ties don't damage them.
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