I would probably be inclided to fit the pins where they were going, then put a blob of paint on each one, and close the bonnet onto them. This marks the underside of the bonnet, allowing you to drill a single hole, big enough for the pin to come through.
Assuming you have the templates, these can then be marked up with the pin centreline, if it is not already, and the layout transferred to the bonnet (sharpie markers are your friend...)
How to cut it? I would probably use 2 hole saws, and join resulting holes with the jigsaw....
hth
Mark