1. You won't have problems.
Https://plailect.github.io/Guide/get-started
2. You can use JKSM to back up the save, and inject it later.
3. Yes, it installs cias. You just need to place them in your SD card. You can also use freeShop to download and install games directly on your console, and not have to worry about finding cia files.
4. Replace boot.3dsx with the original one from smealum's page, so you can get to the homebrew launcher. Then you can choose to exit it and be on sysNAND. Then change the theme and menuhax will be uninstalled, and you can get to sysNAND normally after that.
5. The point of this section is to get your console to the latest firmware. If you have a NAND backup you can use that, or restore from your emuNAND backup, and/or update from System Settings. Just look for a path that involves you getting to the latest version and you're good. If you want your emuNAND data you'll have to do the Move emuNAND section. Note that will reset your firmware to whatever emuNAND had so it would be a waste of time to update your system before doing this as you'll just have to do it again after. If you just think through it it will make sense.
6. None, unless:
- you use the wrong region or wrong firmware files
- you let your battery fall out or let your console run out of battery while writing to the NAND
- you otherwise do something not in the guide. Mostly should be obvious that it's a dumb thing to do. For example I saw someone try to update an N3DS on 2.1 with a game cart, someone else did a system format of a 2DS, etc.