Steve,
As you have found, there is an inherent weakness in the Dragonfly gearbox (which can render the main casing totally useless), and my previous suggestion was aimed at recovering the original case. However, if you have a better replacement case, then build everything into that case, but take on board that the original weakness still exists. The most likely sequence of events with your original box was that the auxiliary shaft rear support fractured, operation of the kickstart then levered the auxiliary shaft out of the lug in the main casing. So, to prevent it re-occurring, do a dummy run of re-assembling the auxiliary shaft and the rear mounting plate, with a view to strengthening the mounting plate with a run of weld down the outside of the slot (with a bit of luck, there will still be room to fit the cross pin - if not, leave the pin out).
Before finalising the re-assembly of the box, check the mesh of the dogs in all 4 gears (especially top gear) - some of the later Dragonfly boxes suffered from shallow engagement of the dogs causing the bike to jump out of top gear when under load. This can be easily overcome by shimming the input bearing - get back to me if you need more help on this,
Regards,
Eddie.