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They aren't quite a straight swap assuming its the decent S3 intercooler your fitting as seen on the 2007-2009 S3 and not the inferior intercooler on the CDLA engined Leon Cupra R/S3 from 2009-2012 which has the same thicker core as the older S3 intercooler but with the small plastic end tanks as seen on the original Leon Cupra intercooler rather than the large metal end tanks as on the early 2007-2009 S3 intercoolers. Different bolts are needed to fix the stainless S3 core to the stack than the original plastic screws on the Cupra intercooler.
Also, both variants of the S3 intercooler use different boost hoses to the Cupra intercooler.
Fitment/space wise, both S3 intercoolers will fit no problem as mentioned above.
How much did you pick that up for if you don't mind me asking?
Can you use the hoses of the stock intercooler or are they a different size due to the difference in end tanks?