Can I flash a emuNAND backup or it has to be a sysNAND backup?
Again, you would have had to kept an original backup , OR have an emunand that was only ever updated via internet. A never updated (freshly formatted) emunand is an exact copy of your sysnand. BUT if you ever installed a firmware update to your emunand with a cart, rom, or cia files, then your native_firm is toast and you would have a black screen brick if you flashed it to sysnand. If your emunand was updated via internet (through system settings, not from a prompt that says an update is available), you don't have that problem, and yes, you can flash that to sysnand.
BUT... this brings me right back around to my original concern. Every guide I have read has said to backup your sysnand, then save a copy of everything on your SD card at that point to a PC, BEFORE you ever formatted the emunand for the first time. If you did that, you'd have a sysnand backup. Why didn't you? You can NOT flash an emunand from another system into your own system. Not without modifications that you are unable to do at this point (you need to have a nand.fat16.xorpad for both your 3ds, and the donor 3ds (and they must be the same type of 3ds model (as in o3ds, n3ds, 2ds).
Just one question: Can I use Gateway or Sky3ds for booting the emuNAND?
At this point, it wouldn't hurt to try, but I seriously doubt it. If you could possibly launch the HBL via Cubic Ninja (which... you would have to already have set up, since you can't get on the internet with it) then you could work around this, especially now that you can launch the Gateway menu with a 3DSX file from HBL. Again, I really doubt it though
. The exploits rely on things that simply aren't loaded in safe mode.