Off the top of my head :
The 11E has grey painted steel cooling cowls on both sides, not cast aluminium, has different gear ratios, has the fan on the clutch side keyed onto the end of the crank and not screwed on the dynastart. Clutch covers are totally different.
The usuable parts from an 11e engine which can be used on a 9e are : head, barrel and piston, dynastart, crank but it has to be cut down to removed the fan drive, clutch basket and plates. The fan can be used on a 3T and the tin cowls on the later improved 9e as used in the Scootacar Mk11. There are probably more smaller parts that can be used but a lot are scrap hence why Bond Spares used to have tons of aluminium casings and gears that no body wanted.