The plans show the reference as the top edge of the fairing, which is what I did on mine. Of course the point is to get clearance from the tail spring. I believe I just left that as a rough opening until I got the landing gear and could verify the clearance I needed.
Theres nothing to stop you from trimming it more if you want more clearance from the fairing. The spring curves down and away from the fairing farther aft so its only that very forward part that needs attention.
FYI: Section 40B (landing gear and engine mount) does not specify a minimum clearance between the rudder bottom and the tailspring. Mine came out to about 3/16 which is pretty close. Hopefully I will never land hard enough to flex the spring that close to the mounting bracket.