Savedatafiler should work. You should have it installed as a cia.
First, remove the header from your rom and change it back to .3ds. Then put the save that you want to convert in the 3DS big SD card with the following name "000400000FF40A00.sav" (that's the id of savedatafiler).
Boot into emunand, press select and choose the game but don't start it. Instead, start savedatafiler. Highlight CTR-Card (make sure it doesn't say "broken" next to it) and press Y, then A.
Close savedatafiler, remove the red GW card. Put the micro SD back in your PC, and put the header back in your ROM, and change it back to .3dz.
Again in emunand, press select and choose the game but again don't start it. Start savedatafiler. Go to the SD tab. In there you'll see a list of all the saves you've decrypted, which should be only one unless you've done this before. Highlight it, hold L and press A.
Once that's done, turn off your 3DS, and put the big SD card in your PC. The file 000400000FF40A00.sav will now be your new save. Give it the right name for your game and you should be done.