So after I saw the link I got curious. My cowl's square opening are covered by a mesh and not blocking the openings. By punching through the mesh I may gain a little airflow but a quick test showed air is passing through the mesh so I left it along.
However, on the passenger side there is a solid plastic cover underneath the mesh. I did drill some holes on this plastic piece not directly under the openings but just to the side of them so water don't get through. Interested to see how this will affect the temperature.
Here is another link to a fresh air mod.
http://ultra.litpixel.com:90/BoarderPhreak/pictures/Fresh_Air_Mod/
Where he mentioned the black air intake cover is the piece I drilled holes in.
Jim