Hey Crash,
I get a folder cut some 2-3" wide strips. I tape them to the plane where a hole has to be in the cowling. Make your holes, then with the strips still on the plane mount your cowling(with the proper depth of course) then mark your holes on the cowl. I use a small pointed stone tip on my dremel tool to cut out the holes to my marks. I use 220 grit sand paper folded small and litely sand the edges from the inside to get rid of any strands and rough edges. If you want you can run a little CA on the inside to reseal the edges of glass(not necessary), and thats how its done in the mohawk hangar. Hope this helps.

SPUDs out.........see ya