There IS NO 10.4 yet. Not on the US site, anyway... Latest emunand is not supported on N3DS. It is supported on O3ds and 2ds. To update N3ds to 9.5, use sysupdater and files from a certain ISO site for 3DS consoles.
You don't update ONLY the firmware files when upgrading rxTools. You update every damn thing that it comes with. This includes the .3dsx. This includes the rop (if you use MSET).
Save files (
@vkyuu)... first question, do you know which folders inside of Nintendo 3ds/ belong to your emunand? Are they named exactly the same on both cards (don't just look at the first folder, but the folder inside of it as well). If so, it is as simple as copying and pasting stuff from one card to the other. If they are different, you may need to use savedatafiler.