Biggest thing is to take your time and remove small amounts. With the engine mounted in the proper location tape a piece of card stock to the fuse so that it hits the valve covers or any part that will stick out of the cowl but does not get in the way of re-mounting the cowl. Cut the card stock so that it goes over the engine with some clearance. Now remove the engine and mount the cowl. Use the card stock to draw the opening on the cowl. Remove the cowl and cut the opening but leave yourself some room so cut inside your line. Re-mount your engine and start test fitting the cowl removing small amounts at a time till you have a good fit. Do not remove the card stock from the fuse until you’re done because if you move it you will loss the alignment.