I managed to get 100% on the PS4. What I remember doing was:
Passing every mission on Normal -> This Unlocks the Hard difficulty.
I grabbed every XOF badge.
I grabbed all the Cassette Tapes.
I passed every mission on Hard -> And what I did was play every mission on Hard twice. So in every mission I get an S-Rank (**Both in Medium and Hard this is required to get 100%). And then I **play them again to set a score for the time-trials etc.. (If you have gotten an S-Rank before just chill out a little bit and have fun - try new things :D)
Then I remember being stuck at 90 something % so I googled and I needed to at least do one challenge in the Ground Zeroes Mission. For me it was Marking All Enemies (but I guess you can choose whichever one you think is easier). I think that Marking All Enemies is kind of fun and easy so it's an easy way of getting the challenge done. I did it on Medium in my PS4 playthrough(I have 100% in the PS4) and currently on my PC playthrough(I have 90% on my PC) I did it on Hard.
It doesn't really matter the difficulty. Just yesterday I played on mission again on medium and another on Hard (missions I had only completed once) and the percentage went up and more trials were filled.
I consulted this guide to achieve all this (Check it out if you want):
Ground Zeroes 100% Guide
Hope I Helped!