I suppose there are many ways, and I suspect that you will get several suggestions from your post. Here's mine.

I usually cut some 3X5 cards into 1" (or so) strips.
Put a hole in one end of the strip that is the size of the screw hole for the cowl.
Locate the hole in the card strip over the blind nut - you can use a screw for this purpose.
With the long end of the card located aft on the fuselage, use blue painter's tape to fasten the card to the fuselage.
Repeat this process for each screw hole.
Remove the screws (if you used them to locate the cards).
Install the cowl where you want it, but be sure that the card strips lay over the cowl, not under it.
You will now find that each mounting hole is very accurately located by the hole in the card.
Mark the holes on the cowling and then use whatever process you think appropriate to drill them.
It should fit right up.

If I have forgotten anything; hopefully, someone will point it out.

Good luck