Running your air cooled engine with the cowl removed is harder on the engine than you may realize. Uncowled, air is blown over the cylinders and not through the cylinder's cooling fins. So the bottom of the engine is left to heat-soak and the top is cooled. This uneven heating results in distorted cylinders which damages the cylinders and the moving parts inside the cylinders.
Continental recommends fabricating a scoop out of sheet metal for use when running up the engine on the ground when the cowl is removed. This provides a safe amount of airflow for runups and can usually be constructed in a way that it is out of the way for most maintenance procedures. (Drawing credit: Continental Motors)