This is probably a method many of you already use, and it’s the one I prefer as well.
Before mounting the engine, I make a paper template with a cutout that represents the exact clearance I want between the engine and the cowl all the way around.
I then mount the engine on the airplane, place the template in position, and mark its location on the fuselage with a pencil. That way, even after removing the engine, I can put the template back in exactly the same spot using those reference marks.
Once the engine is removed, I start building up the cowl area by adding wood blocks until I have a solid structure to work with. Then I reposition the template using the reference marks and transfer the same opening onto the wood blocks.
I’ve found this method to be fairly accurate and repeatable, with very little error.
The following photos should help illustrate the process better than words.