I drilled the marked holes in the bottom cowling, then reinstalled the cowling and checked the fit, and taped it to the fuselage. I then removed the top cowling and drilled the holes through the hinges.
The next step is to attach the horizontal pins but I noticed in the plan I made a mistake with the left side. The forward-most part of the bottom cowl hinge should have an eyelet. Mine doesn't.
I doubt in the long run it'll make a difference but there's really no reason for me not to order another piece of hinge and do it right.