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Here's the formula for calculating the scores inside the _ScoreRun function

Note that time and time_without_menus are measured in tenths of a second. So 1 hour is 36,000 units, if that's menu time then that means 3600 points lost, if it's in-game time then that means 7200 points lost.

You can also see how many points each difficulty setting is worth (excluding Combat Difficulty) inside the TestScoring function

Currently Normal gives 4570 bonus points, Hard gives 9980 points, Extreme gives 12080 points, and Impossible gives 13795 points.

Normally you only need to know the point values for the preset difficulties, but you can see the scoring for individual flags in the ScoreFlags function here