I'll be posting here too for more visibility.
I updated my emunand from a clean 4.5 emunand (confirmed it was GW3DS). At some point during the update, it said it failed, and the system rebooted.
When I entered gateway mode, I had the new themes and the new firmware features, however going into settings it tells me 4.5GW firmware.
Tried to run smash, which requires 8.x, and it ran without asking anything.
However, I cannot access eShop, which is the big problem.
Updated via smash even though I had the 9.x features, it apparently let me do it and it worked, I still kept the 9.x features/UI. Tried to update it through system menu for the 9.x, again error.
Then I scrapped the entire emuNAND partition, formatted emunand, and began from scratch. Got 4.5 GW3D emunand again, this time I updated with smash from 4.5 clean to 8.1 first, which gave no issues whatsoever. Then I went to system to update to 9.x, again the same error.
It simply won't let me install update 9.x. Spent 3 hours doing the same thing over and over.
I need some help. Does the 3DS sd card need to be formatted in some specific way? I have no idea what to do.