One simple test worth trying, and I know others will decry this, is to align the prop on TDC of the engine. My non-expert opinion is that if there is any imbalance brought about by the prop (even after balancing) it's probably best to have it on the same plane (non-aircraft) as the inherent imbalance that single cylinder engines have. One imbalance is better than two (one inherent to the engine and an introduced one from the prop).

From my own personal experience, including those of my friends, is that you'll get higher peak RPM keeping the prop aligned with TDC.

Others will disagree on either one or both aspects of my theory, suffice to say I've measured improvements on multiple engines and it's the results that count (even if the theory itself doesn't hold up).

Put the engine at TDC and ensure the prop is aligned vertically through the same plane as the piston/rod/crank throw. It costs nothing to try....