I just spent a good amount of time messing around to fix this, I even CTRtransferred my 3DS to download the update, and messed around trying to rebuild the CIA, only to realize the issue is that the CIA floating around on the internet/in this thread (MHXX1.4englishV5.cia) just lost the minor version number when being rebuilt. I never figured out how to rebuild the cia properly, but just fixing the already patched cia was pretty easy.
Code:ctrtool --contents=contents MHXX1.4englishV5.cia makerom -f cia -o game.cia -minor 8 -content contents.0000.00000000:0:5 -content contents.0001.00000001:1:1
Anyway, a year later, here is the fixed cia, and also the unmodified update I CTRtransferred to dump.
https://mega.nz/#F!OI0gwIDL!Gpoda8X37dXEqMVdhpXimQ
Came to thank you for this fix, this is the definitive and most reliable way to patch the game with this cia. Search no more. Thank you pal!!!