In order to provide PROPER cooling for a cowled engine you will need an area for the heated air to exit that is 2 - 3 times the area of the inlet air. If the muffler is also fully enclosed, as in your case, I suggest using the 1:3 ratio for cooling.

Usually, the exit hole will be in the bottom of the cowl where the exhaust extensions come out. Since you already have holes in the sides of the cowl, the hole underneath may not need to be that large.

You may also want to consider mounting the cowl so it is slightly forward of the fuselage. This way there will be exit holes all the way around the cowl.