Cant i use the save on my retail card/ eshop version?
No, this method required the use of a gateway card, the save will not work via any other methods.
Actually, I tried it last night, and yes you can with the eShop version. However, you still require a Gateway 3DS to get it up and running.
I started off by creating a duplicate of my SD card, contents and emuNAND, but you don't need to do this if you don't mind losing your save.
This is essentially what you need to do.
1. Inject the save file into a rom using one of the tools in the first post. I used a USA rom to match my region. I don't know if it'll work otherwise.
2. Put that rom onto your microSD, then into your Gateway red card, and into your system
3. Boot into Gateway mode (emuNAND with most recent firmware required)
4. Download the Save Data Transfer Tool off of the eShop
5. After returning to the main menu, select your Pokemon rom using the multirom menu.
6. Start the Save Data Transfer Tool, and follow the onscreen instructions.
7. Enjoy