I don't know if this will help you, but it's a idea.
Create a invisible tile, or object or anything at the start of the stage at the same position as the player. as the player moves you calculate the distance between the player and this object, the longer the distance bigger the score, and this will apply if the player is going up or down
And since you want the score to decrease if the player goes down, instead of setting the invisible object to the same position as the player's, set the object at the bottom of the screen. that way the player will get closer to it every time he goes down