Hi there!
I balance helicopters for a living, the lister is child's play. I understand single cylinder engine balance quite well. I've come to the conclusion that the balance of a single cylinder engine really needs to be done while running. While not required, it might be slightly better to do it at partial load. If both flywheels are consistently made, they then any unbalance will offset each other. As they are mounted opposed.
Install 'em, run the engine and then balance it, via the methods contained in some threads/posts on this forum. If you balance the flywheels first, you have not accomplished anything helpful on a single.
Briefly: A Lister's single piston's inertia can be offset by a 100% counterweight. However, that full counterweight will then cause horizontal "shuffle", as there is no horizontal opposing force to that counterweight. Picture the counterweight at the same level as the crank, it's inertia will pull the engine that direction!
Soooooo, a counterweight is generally "about" 50% of the reciprocating mass. For many single cylinder engines, a 53% "balance factor" works well. This results in an engine that has equal up/down and fore/aft vibrations. And done correctly, is generally considered comfortably smooth.
A single will never be vibration free without some form of trickery! (for example, a single or better yet, pair of counter-rotating balance shafts) There are other ways to make a single mostly vibration free. None of these methods apply to us, ignore them.