Holy cow, there's a lot of content here. It's really impressive that you got this much out in just 48 hours. Did you sleep?
Some initial comments:
- Your combat system just is in that annoying grey area between "streamlined and easy to run" and "crunchy and complex" where the rules are fairly simple but it's still complicated and annoying to play out an actual fight. If the game is about the people managing the missions, it would make much more sense to have a single die roll resolve the combat and be done with it. You win some, you lose some. Sometimes you beat the super powerful rock monster and sometimes you die to the monkey with a slingshot.
- Your humor is appreciated and it breaks up the big walls of text.
- You never explain when to use skill checks or what benefit they give you. You say "Roll 1d6 and add your stat" but never explain what value is "succeed" or "fail".
Honestly I really like the theme. With some adaptation, I would definitely use this as a minigame between Uncharted World missions.