Answer from Van's on the trim area in the large opening in the bottom cowl was to eyeball and trim to provide relief for the top cowl so that's what I did. (step 1 final)
Did a lot of sanding to clean up excess resin at flanges and joggles. Trimmed flange to 5/8". (steps 2 and 3)
Clamped top and bottom cowls together, marked, and drilled #40 hole at inboard locations. (step 4)
Cut and trimmed nose gear slot, exhaust opening, and gascolator access opening under bottom cowl. Trimmed oil cooler opening. (steps 5 through 7)