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The enginehead is facing backwards on a Fury, and is facing forward on a Freya.
On a Fury the muffler is on the right side, and on the left on a Freya.
The only thing that will change regarding the muffler is that the pressure tap will be at the bottom of the muffler, and since you´re using a YS it wont be a problem - might not work well with a OS with mufflerpressusre though.
Not sure if the #998 will header will fit your Freya, looks slightly different from the #999.