In that case you can use HBL to load JKSM's Save Manager and backup any digital game saves you'd like. Since it's only running in user land and not installed as a CIA, you won't be able to back things up like Mii Plaza or Streetpass data. Your friend code will also change.
But ultimately you would use your wife's 3DS, install A9LH on it (is it an o3DS or n3DS?) and then purchase and exploit Fieldrunners. Make a backup of her 3DS using Decrypt9 and then you'd transfer her console to yours, replacing everything on your console. You'd then hack your 3DS by dumping your NAND, modifying it and writing it back and then downgrade to 9.2. Once you have A9LH all set up on your 3DS and you're back on the latest system firmware, format your system so that you can set it up with your own NNID, re-install your games and then use JKSV to import your saves.
After you're done with your own and have formatted it, then set your wife's up as new and sign into her NNID. If she wants to keep A9LH, then simply restore the backup you made. If she does not want A9LH, then restore the 9.2 backup made during Plailect's Guide and choose FORCE instead of KEEP A9LH, then re-update to the latest software.
Total process time would be a few hours (1-2 to hack hers, 2-4 to hack yours).