1. Download and install SnakeBite Mod Manager: https://www.nexusmods.com/metalgearsolidvtpp/mods/106/
Now you can install mods acquired from NexusMods (I know, Nexus sucks lol)
 
2. Download these two mods:
Infinite Heaven: https://www.nexusmods.com/metalgearsolidvtpp/mods/45
IHHook: https://www.nexusmods.com/metalgearsolidvtpp/mods/1226
These are the only two mods you absolutely need.
 
3. After installing everything, launch MGSV. Open the IHHook menu by pressing F3 when you get to the ACC. Here, you can make changes to many of the game's mechanics and variables, as well as enable new features such as Skull Unit events. For a full list of features, check out the Infinite Heaven documentation here: https://www.nexusmods.com/metalgearsolidvtpp/articles/5/
 
Other mods that I like:
- Uncle Jimbo's gunpack (2K version) -- Complete overhaul of the game's weapons.
- MagazineOSP IH add-on -- Generate magazines by reloading weapons.
- More Animals
- MGS2 Solid Snake Sneaking Suit (Vanilla) -- Visual mod only.
- I Can't Believe It's Not ReShade 1.2 -- Visual mod only.
- S plus plus Soldier Mod -- Lets you find S++ soldiers in singleplayer.