I use a Dremel with a cone shaped abrasive bit. I can use the tip of the cone for more precise stuff or push it in to the larger diameter area to remove material faster.

Try to start small and work up to the final opening size. It is easy to remove more material if needed but impossible to put it back.

One trick is to use cardboard taped to the side of the fuselage that extends out over the motor and other areas that need to be cut. Experiment with cutting the cardboard until you get it just right. Then remove the engine, put the cowl in place and trace the openings in the cardboard on to the cowl. This will get you very close and will likely only need some fine tuning. I wish I had some photos or drawings of this to post.

The Cherokee should be pretty simple. On my glow version, I made a large U-shaped cut out to clear the muffler and nose gear. Then a simple opening for the cylinder head and a round hole for the high speed needle.