Aftermarket intakes can improve air flow into the motor a lot, because the OEM intake system is designed to baffle and reduce intake noise. So the downside of an aftermarket intake is possibly increased induction noise. BUT, I'd imagine that would show up right away and NOT years down the road, as well, I've never heard induction noise that sounded like a vibration.
The exhaust may be banging up against something as it vibrates. Look again, for clearance all around the exhaust parts, as well as the heat shields around the exhaust.
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