Your main problem most likely will be your CFW which won't necessarily support the latest firmwares. You'd need to switch to another CFW such as Luma, but they don't support old entrypoints anymore, they use new ones that are tons better (no more menuhax that fails 1 time out of 10 and that doubles the boot time).
On the new entrypoint, b9s, an emuNAND is no longer needed. You can keep it of course, but it's probably going to bring more problems than solutions (like when you want to upgrade your SD card, you have to think about your emuNAND...).
The guide is here
https://3ds.hacks.guide/
I guess the best plan for you is to disable menuhax, follow that guide to the end to get b9s and Luma, then once everything is working (but everything is working on your sysNAND which is not where you have all your data), you have a choice:
- tell Luma to use your emuNAND
- move your emuNAND to your sysNAND