Thank you so much for posting this.
It gave me great insight into fixing my own ezflash omega. I created my own case for the ez flash omega from an old gameboy boy. I did everything like you but that didn't solve my issues. Then I came back to this post and read "the case was made pretty bad...
Title says it all. On a 3ds xl with sysnand 4.2 and emunand 9.4. I know SSB requires 4gb card when using a rom but with a retail cart, that isn't supposed to be the problem because I can play it without a 4gb card on sysnand 9.2.