After retrying reformatting and trying again I was able to update my emunand correctly with the theme support available.
I still can't go online with my 3dz format games but I am guessing that is because I am not using the latest emunand which is 9.5.
My retail Monster Hunter 4 Ultimate game works fine online and that is all I care about right now.
Thanks for explaining everything to me.
I wish someone would do an easy tutorial because I am sure there are people who were stuck in the same situation as me.