I'll give it a go tonight. Many thanks.I would downgrade the N3DS, set up CFW and do a system transfer after that. If you update your N3DS to the latest firmware, you will to use need Cubic Ninja or Ocarina of Time, Smash Bros or Pokemon Super Mystery Dungeon and a Save Dongle (Action Replay Powersaves) to downgrade. It's easier overall to downgrade with the browser which you can do on firmware 9.9.
You can follow this guide to downgrade and get Arm9loaderhax and CFW set up on your N3DS. After you've got CFW set up, you can update to the latest firmware and do a system transfer without issue.