Firstly, have a look at Circle Circus or World Runner scripts. It solved partly the problem. Decide a reference altitude of the ground groundY then adjust every shape offset with this value.
But the core issues is still here. With games like River City Ransom or Double Dragon or Ninja Turtle in which characters truly move in three dimensions (xz plain + jumping) there is just no way to calculate those values from just 2d position x,y. In this case we need to know the nes ram address that stores the character's current altitude y. Only with that info we could finally calculate the other two value x,z and truly reconstruct the 3d scene of the game.