I'm just throwing this out there. Is the issue noise, vibration, or both?
If it's just noise, I don't see the firewall insulation. Maybe it isn't clear in the pictures, or I'm looking in the wrong place. That insulation cuts down on noise. Other than the intake, is the engine noisy outside the car? What sort of noise is being heard in the cabin? Intake? Exhaust? Internals? Accessories? Mechanics have a stethoscope that can be used to identify noises. Some things, like that dipstick handle could be too close and hitting the firewall; or, something else could be hitting against the engine, if proper clearances weren't allowed for.
If it's vibration, I'd recommend starting with the engine itself. It seems that the engine is running smoothly, but is it? I'd then check the mounts, both engine and transmission. Is the rubber or poly all good? If they're solid-mounted, that could be the issue.