I'm sure someone has nifty graphics showing this way, but here it is in words:

Mount engine and muffler in final resting place. Using file folder or similar cardboard, make a template that attaches to the fuselage behind the place where the back of the cowl is going to be located. Fasten this cardboard securely at the rear end with masking or other tape. It has to at least be larger than the engine cylinder head and muffler.

Trace around the cylinder head and muffler onto the cardboard with a pen or pencil. Cut out what you just drew with scissors. These are the holes you need to cut in the cowl.

Remove the engine and install the cowl with the template outside the cowl. Tape the front of the template into place and trace through the template holes onto the cowl. This is what you need to cut away. You'll need to do a lot of trimming and fitting, and a drum sander on your rotary tool does fine for this.

I use those "RotoZip" drill-like bits (used to cut holes in sheetrock) to cut fiberglass parts, but I run them in my high speed rotary tool.

Do this outside since fiberglass duct is really nasty stuff.