I did the same thing, I used Xenoblade to update to 9.4. Just be sure you're holding d pad up while launching Gateway mode. It doesn't really do anything special - it just disables the firmware spoofing so that the cartridge doesn't think you've already updated.
Sorry, to my knowledge there is no way. rxTools could get most of your stuff over manually, but we don't have it working on n3DS right now. You're better off doing what I did - just backup all your saves and move your games over. If you need to update your emuNAND to 9.4 to get Amiibos working (note that 9.6 is the latest right now and isn't supported), just use either Xenoblade or any other 9.4 game.