The original questions were: "Will that make a conversion to a 12 volt system necessary, or can I make the new engine & charging system compatible with the original 6 volt setup?"
A conversion to 12v is not necessary, and it is easily possible to make the new 12v engine compatible with the original 6v set up.
use the 6v battery
use the 6v engine's clutch housing, flywheel, and clutch assembly
use the 6v starter
use the 6v coil
use the 6v generator and all the other electrical parts from the 6v system
Changing to 12v is not difficult, and it would be just as reliable as the original 6v system. But, changing to 12v is not a necessity.