If your sysNand is working good and you are not banned from Nintendo servers (can you access the eshop?) I would do the following:
1/ Update your original firmware (OFW) to the latest version 10.1.0
2/ Update your joycons in the settings menu
3/ Make sure you have created your own profile and deleted those from the previous owners
4/ Turn off your Switch, backup your "licence.dat" and "boot.dat", and eventually others files from your SD card you want to keep
5/ Format it using "Guiformat FAT32" tool that you can find on Google, then copy the "licence.dat" and "boot.dat"
6/ Turn on your Switch and press Vol+ as soon as you see the SX OS screen to enter the bootloader.
7/ Go to options, select SX Core, and "cleanup" to remove any trace of modding (even if we don't know what it is doing exactly)
8/ Select Nand and dump your Nand keeping the default settings (Boot0, Boot1, Raw Nand) It will take around 2h to dump the Nand so plug the power to your Switch
9/ When it is finished, turn off your Switch and copy the backup to a safe place like your computer or an external HDD (files to backup are in sxos/backup)
10/ Turn on again your Switch, enter SX OS bootloader, and create your emuNand, either with hidden partition or files on SD (I don't know the pros and cons) It will take around an hour.
11/ When it is finished, boot to CFW on your emuNand to check it is working fine.
12/ Turn off your switch and copy on the SD card all your homebrews and backup games.
Hope this will help.