I haven't tackled too many of the harder-version missions in the 40s, but I can see how they might be tough:
[Total Stealth] Pitch Dark (Africa, where you go to the oilfield and sabotage two things)
[Total Stealth] The War Economy (Africa, where you go to the airport because an arms dealer is meeting with a general)
[Extreme] Code Talker
[Subsistence] Occupation Forces (Afghanistan, where you find an intel file about a commander with tanks then deal with said tanks)
[Extreme] Sahelanthropus
I already S-ranked the Extreme versions of Traitors' Caravan and Metallic Archaea thanks to the hangar at the airport + Quiet.