Good that you got the engine to run.
The wire going from the starter to the ammeter is the main power wire for the system, for anything other than the starter, that produces, or uses power.
On a Cub with a magneto, that would be the charging system, and the lights.
The wire has to be connected so power can go from the generator to the battery, to charge the battery.
My opinion is that the condenser in the magneto can't make any spark if shorted to something, it is too small to store that much power.
I've never seen a Cub or automotive condenser make a spark.
The only thing near the magneto that could have made a spark to ground if you touched it with a wrench is the post on top of the starter.
Maybe you somehow touched it with a wrench that had the other end inside the magneto, I don't know.
Always keep wrenches away from the starter post where the battery cable connects on, when working on other things, with the battery connected.
Does the ammeter show charge when the engine is running at speeds above slow idle ?
