Russ,
My Wife and I had a discussion the other day on if we should drill holes for the badges. We chose to go with the same solution as you did. Our stripes will also be white, so the clear adhesive will work well for us too. I'm not sure if the dimples on the hood and trunk lid are for placement of the holes for the badges, but they were not centered.
You Cobra is really coming together very nicely. It won't be long now.
Russ C