Ehhh, sky3DS is only good if you need to downgrade to 9.2. CFW is waaaay better, and free!! I really think there was some kind of hiccup with your SD card when you created Emunand. I think this will work: use 3DS multi Emunand creator or Emunand Tool and inject your NAND.bin (from Section 2) into your Emunand. Then inject BBM or devmenu to Emunand and try it.