didn't do it myself but I have seen the nut ground down on the one side that had been contacting the casing.
Some nuts seem to be thicher than others and some are chamfered which helps.
There must be something wrong with the assembly! The spacer between the bearings must not be less than one inch. If you space the crankcases apart, will the cylinder fit anymore? Will the crankcase fit properly between the engine plates? Ron