You should be able to adjust the CO trim in the ECU to compensate for adding the airbox lid but not if you have lamda sensor or so I have read. I don't have lamda on mine anymore so its not an issue for me.
The induction noise is part of the experience of the big 4 valvers
but you could try adding the tank liner back.
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S4 Fogarty, S4R 07T, 748, Series 1 Mirage