How to extrude in both directions and trim circles from a surface? Please help

Hello all- 

I am very close to having the definition, I need but I need to trim out circles that are aligned on the lunch box grid out of the surface (creating a swiss cheese affect). I am having trouble with the following two steps: 

A. Extruding the circle curves on both sides to get perfect circles cutting into the curved surface. Project will not work because the circles become warped.

B. I need to trim out all of the circle interiors so that I am left with a surface with many holes. Is this possible? Can I get rid of the interior of the circles without having to do it manually?

Thank you so much for any advice!