I can see why nobody is fond of fitting the Sonex cowl. It's tedious and imprecise. Yes, you can fix fiberglass if you cut out too much, but who wants to do that!?
I used painter's tape to mask off the first several inches of the windshield so the cowl would not scratch it as I man-handled the cowl into place.
After some more rough fitting I marked the back edges of the cowl for cutting and cut with my Dremel cutoff wheel and then a drum sanding attachment on my hand drill.
Then I got the front of the cowl aligned with the prop hub spacer and attached it with drywall screws, as suggested.
I have been using the rear edge of the cowl, where it meets the fuselage side, as-is from Sonex. But I think I need to trim that down a bit to get the bottom of the cowl to fit better to the underside of the fuselage, and to get a smoother transition between the cowl and the fuselage at the point where the gear goest through the cowl.