Hi Mark,
My airbox is standard and the sides seem in alignment looking from above but,
Looking from the side on mine the contours of the bodywork do not line up with the airbox, so the seat unit is to far forwards and down.
Maybe the blocks under the seat pad need to be raised a bit to make it higher, not sure how to adjust it backwards. Mine also creaks when sat upon, and I'm only 11.5 stone
Going for the 6000 mile service in Nov. so will ask then, if they do move it back the white parts wear the paint has worn away will be more visible though