Tonight I sanded away the high points and painted the inside of the cowl scoop with Upol Reface, a high solid content filler primer.
I then sanded the attach flange around the cowl opening and cleaned with Xylene in preparation for epoxy resin and Aerosil, which I lathered on the flange. I had already applied broad insulation tape to the scoop edges, so when the filler primer was set enough not to run, I clecoed the scoop onto the cowl and smoothed the transition along the three sides. I then sanded sides of the cowl down to about 6" from the air intakes and layed up a broad area of epoxy and Aerosil to smooth the transition between the top and bottom of the cowl. Later I will sand this back and use the ultra thin cutoff wheel to separate the halves again.