I understand walking away, because sometimes we just need to clear our head and take a fresh look. The firing order is 1342; If you told us you had to move all 4 wires over one notch to get it to run right, we would know that something was slightly out of alignment. But when you say you have to switch wires 1 and 2....the Cub wouldn't actually run correctly. That is not possible that someone changed the firing order on your cub to 2341....so the wires have to be crossed. Are the wires in good shape, I heard (what may be an urban legend) about the spark actually crossing over to the path of least resistance, and firing the wrong plug once. But I don't think that could actually swap two cylinders, you'd just be firing one of them twice. Look very hard at the wire routing and condition, and you will solve this mystery.
'52 Cub ("Great Personality") 148xxx
'48 Cub with FH ("Gunny Cub") 38xxx
'57 Lambretta (a slow work in progress)
'74 Triumph TR6 (Mama's toy)