You may be dealing with a valve to piston clearance issue.
The Mahle valve pockets are designed with a pretty close perimeter tolerance. The stock intake valve is 46 mm mm and you state that your intake valve is 47mm. I may be experiencing a slight interference on just one or two valves.
Quote:
2.4S original cams
Ø90mm Mahle pistons
Intake valve: Ø47mm
Exhaust valve: Ø40mm
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