Tape pieces of poster board (available at art and stationary stores) on the fuselage without the cowl, extending past where the engine is located. Make your cut outs in the poster board. Make the cut outs tight. Without removing the poster board, remove your engine and mufflers then install the cowl with the cut out poster board outside the cowl. Mark the cowl through the holes previously made in the poster board. Adjust the tight hole size for better clearance after the primary cut and fit is done.