Shouldn't get any running issues as severe as you describe.
Agree with some of what has been sais above.
On a Classic the standard airfilter is good for about 300-320BHP.
If you want 340+ then need to change to an induction kit.
Did you disconnect the MAF and/or battery when you changed.
If so you may have a faulty MAF and the ECU cannot re-adjust to suit the fault.
The ECU learn's over a long period of time to work with a partially faulty MAF. If you do an ECU reset or disconnect the battery the MAF values return to default and you get rough running.
I would suggest swapping back to the stock airbox to see if it cures the fault.
The extra noise is the sucking and dumping of air normally hidden by the plastic box of the standard airbox.
On the subject of HKS Filters, I have found these to give very poor filtration and have seen 2 cars with dirty or damaged MAF's after using them.
My recomendation for Induction kits are Apexi Power intake, K&N or RCM
For Panel Filter 'Green', K&N or JDM STi,the Green filter has very good flow for a panel filter.
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