Since I haven't built mine yet, can't answer, but...
Why deviate from the instructions? It's just asking for trouble unless you can see that they are incorrect. Since the fairwater is a little tapered, it probably won't fit in the deck correctly if you do that.
But basically, mark where the cut is to be and put a piece of tape around the edge of the cut, tape on the "keeper" side.
Spray the scrap side a color you can see easily like black.
Remove tape. Cut the piece off with a razor saw, leaving 1/16" or so of black painted plastic.
Tape sand paper down on a flat surface and carefully draw-sand the piece across it until the black has all disappeared.