Did you make the emuNAND first, like I said in this post:
If you did, and the emuNAND is a copy of your dirty sysNAND, you can just move the /Nintendo/ folder to the proper location, and you won't have to reinstall anything on the dirty emuNAND.
I did make the emuNAND first. And I have my backups saved on my PC, but I never ended up using them after following the "clean" sysNAND guide you posted. Though wish I saw your post about the Nintendo folder earlier as I have already redownloaded my purchased eshop game and pulled my save from nintendos cloud using the "clean" OFW.
So far so good. I can still play online and connect to the eshop fine using the OFW. As for CFW I ran into an issue where the new Atmosphere emuNAND I installed would not run any NSP I downloaded. Fixed it by replacing the CFW with Kosmos.
If I understand correctly my backup is a dirty emuNAND, my current sysNAND is "clean" and my current emuNAND is properly installed. So my next step should be backing making a backup of the new eMMC boot0/1 and raw?