I installed the DLC .cia pack and for some reason it doesn't work with my eshop copy, it says something like "The SD card was removed" when I try accessing the DLC menu. I had to ~acquire~ a .3dz rom and start a new save file to be able to play the DLC.
To answer the OP, I go into the spotpass...
This might be a problem, hopefully Gateway implements some workaround.
I know they get separated if you do a system transfer from a different 3DS to your emunand, but that is in no way practical.
Damn, I like your username and avatar so much, I wish I could help you.
After launching both sysnand and emunand, how many folders are there inside the Nintendo 3ds folder?
I'm in a similar boat but I still have my old 3ds, so my situation is way easier.
What about those stores that let you return your purchase for any reason in a 7 day window? Could you buy a 3ds, do your transfers and return it?