To make a long story short, I got a CIA for MH4 and its patch to 1.1 and played it. I decided I wanted to download the game digitally from the eshop, so I removed it with bigredmenu(?) and removed any additional files from options in my Emunand.

I went to buy the game and it mentioned "redownload" so I didn't attempt it seeing I didn't buy the game yet.
So I went and bought the physical game and now I can't download the updates without getting errors... I've successfully updated other games (digital and physical) but I can't with monster hunter 4 now...