Well, I screwed up somewhere :/
I did a format emunand again (dunno why, it's late...)
So the N3DS DID sys transferred from my old 3DS but since I created another emuNAND it is not seeing the old files (I guess it happened because I separated the sysNAND and emuNAND)
Since I have full backup of my O3DS I easily restored and everything is still there but now I have to wait 7 days to do another attempt... crap!
Do it like this but DO NOT reformat emunand:
Pre steps:
* Make a backup of ALL you SD card (from the O3DS you're migrating FROM,
don't forget the emuNAND itself)
* Leave both 3DS SYSNAND WiFi settings empty (
a tip from my friend blechner: if you don't have the NANDs unlinked, you will not be able to leave sysNAND WiFi blank as it will be populated back when you fill out emuNAND WiFi. So, unlink the NANDs or clear sysNAND WiFi settings AFTER you have set the emuNAND WiFi)
* Update both 3DS EMUNAND to the latest one and CONFIGURE THEIR WIFI
* Make sure your profile (region), language, region, matches
* TIP: open the eShop at least one time in both consoles and accept the agreement thing we never read! If you don't do it, the sys transfer won't let you proceed!
Migrating:
1) Follow sys transfer wizard and chose migrate using a PC
(make sure you choose the right answers for the sys transfer questions, answering you're using o SD for the O3DS and migrating TO A MICRO SD, for instance)
2) Wait until it finishes and restart both consoles. After restart, the process will take you back to sysnand and fail in both 3DS
2.1) On the O3DS it will simply not do anything else while on the N3DS it'll attempt to finish the sys transfer and fail telling you need to update your sysNAND, *** DON'T UPDATE IT ***
3) Shut down the N3DS, remove both SDs (micro SD from N3DS and SD from O3DS), copy the entire content of your O3DS SD to the N3DS micro SD
4) After copying the ENTIRE content of the SD to your Micro SD, boot up the emuNAND on your N3DS and the sys transfer will open automatically will finalize it's thing. Let it do it.
5) Once the sys transfer on N3DS finishes, it'll tell you so but it won't give you any way to close it (the Home button will not work as well), just shut down removing the battery or holding the Power button for 15 seconds
6) Power up your N3DS one more time and boot up the emuNAND. Voilá! All your O3DS stuff are now migrated.
7) Test everything! It should work!
EDIT1:
Fixing some typos and adding new info
EDIT2:
I will create a mini tuto so more users can easily find this