I got over the intimidation of drilling the holes in the boot cowl. I decided I was satisfied with the fit, and went ahead with it.
I tried to space the holes 3" apart as closely as possible. But, with some interference from riveted splices, and clearance from other things, I had to adjust them. I think it worked out just fine. The main thing for me is to get the holes close enough to hold the panel well, but also to be uniformly spaced for strength and appearance.