Use cardboard templates.

Cut long strips of cardboard and use them to fine tune the openings that you'll need. Then, with the engine in place, tape the cardboard onto the fuselage with the openings you cut around their corresponding engine parts.

Now, remove the engine but not the cardboard strips. Put the cowl in place and trace the openings in the cardboard onto the cowl.

This will get you close if not dead on. I'm sure somebody out there has some pictures of this.

Cut in small increments and work toward your traced lines. It's easy to remove more material but impossible to put it back.

Be sure to have a good air outlet to keep the engine cool also. I think the general rule is 3 times the outlet opening as the inlet? Someone correct me if I'm wrong on that.