Technique One
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First go ahead and mount the engine in place at the recommended distance. Leave the muffler off.

Sometimes I may also need to remove the HS needle and carb too!

If possible slide the cowl into place.

Then put on your spinner and prop.

Align the cowl to the spinner leaving the proper distance from the cowl to the spinner.

Now mark the position of the cowl on the fuse with a panel line pen ( you can remove the marks it makes with alcohol easily! ).

Remove the cowl and engine and use the alignment lines you drew to make the screw holes.

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Technique Two
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If I cannot slide the cowl over the installed engine...

DO NOT worry about making the cowl screw mount holes at first.

Mount the engine on the plane, and make your cardboard cutouts.

Remove the engine and slide the cowl into a rough position. Put a ruler or other measuring stick in through the front of the cowl to get an approximate distance for cowl mounting.

Make temporary alignment marks on the fuse.

Now start cutting the holes you need to be able to move the engine into it's final position.

Put the engine back on and see if you can get the cowl into place.

Keep working on your cowl holes, e.g. the cylinderhead hole, etc. until you get the cowl to slide in place.

Once done, put the spinner and prop on the engine. Align the cowl to the spinner, and mark the position on the fuse...

Sometimes when I am this far along I tape the cowl to the fuse and go ahead and drill the cowl mounting screw holes, as I now KNOW where it should finally rest...