I have just put an S 6speed in an R56 2011 Cooper (which had a blown trans). S clutch and dual mass flywheel were added but my issue is with the p/s axle. Driver side is a new S axle which looks like it'll work ok. Passenger side is a different story. The Cooper axle won't engage with the S trannie - the end seems a millimeter too big in diameter - and the S axle, when engaged in the trannie, is an inch off at the mount on the aft side of the motor (the bearing 'clamp' bolts are an inch to the wheel side of the mount holes).
Has anyone run across this problem? Any ideas?