Hi John,
Welcome to the Forum.
The magneto on your S6 does not have a drive pinion - instead, it has a drive dog that locates in a slot in the drive shaft in the top of the timing chest. This enables the magneto to be removed and replaced without needing to reset the timing. You will find that the magneto sits on 4 steel buttons located in small holes in the top surface of the crankcase - this is to leave an air gap and reduce the heat transfer from the engine. If the buttons are missing, you will find that the magneto does not line up with the drive shaft.
A lot of advice can be gained by joining the London Douglas Motorcycle Club - the Surrey/Hants section meet at Guildford on a monthly basis. We have a least 6 members with S6/T6 models.
Regards,
Eddie.