As the title says, here’s a map and path of the most confusing area in the game with mistles, vestiges, keys, and shortcuts.
The legend on the top left tells all that is needed to be told for the colors. I tried to make it so that the path always returns to the base after a change in elevation. If any paths cross the base is the first time through while other colors are in relation to the base. All of the side items and misc things I ignored since, well, the point of this map is to get to the end for either story path you want.
Note: I forgot about green while putting together the map legend. That’s a Regen Activation Factor.