The Dragonfly has a totally different kickstart mechanism, layshaft and final drive shaft to that in the Mark gearbox - the rest of the internals are the same.
If you fit a Mark gearbox in a 'Fly, you will need to remove the dipstick from the filler cap, otherwise the Dragonfly toolbox prevents the filler cap from being removed.
The damage you have described is not uncommon on Dragonfly 'boxes. I have never understood why Douglas felt it necessary to fit a cross pin in the auxiliary shaft - had the pin been omitted, the lack of a slot in the cover plate would have made the cover much stronger. The shaft being capable of turning wouldn't cause any problems as it would only turn when the kickstart was being operated - when under way, the whole kickstart mechanism remains stationary.
Regards,
Eddie.