You need to be more specific. I assume you have not completed the 5th part of the tutorial completetly since you opted to keep EmuNAND which is fine. What were your exact steps after getting the OTP/installing A9LH?
Did you make sure to get the correct region roms? Sky3DS doesn't support region free but itself, so if you have roms from a different region they won't show up.
Everything you need to know is described in Plailect's great guide. Don't skip any instructions and carefully read and follow them.
The 16gb SD card is fine and I would recommend that you use that one because of the NAND backups you have to make in the process.
Search on that ISO site for "config.cia". Install it with devmenu/bbm/fbi and launch it. In EULA settings change the version to ff.ff then save it. After that you have to power off your console with the power button and it should work after.
Yes you can downgrade the newest firm 10.7 to 9.2 with the Sky3DS+ and Cubic Ninja rom. And you most certainly have a SysNAND. I highly suggest that you very carefully read this guide before attempting anything.