Don't try and link your NNID to the new 3ds, the target system can't have an account already linked to it. Perform the transfer from the old 3ds to the new one and the game will appear on your downloads list once the transfer is complete. Once you've transferred you can use whatever memory card you want.
Gotta love Royal Mail not even bothering to turn up and deliver even regular mail on my street today. My package was shipped yesterday morning first class. Hate them.