How Do I Use /scoreboard To Change Clone or Tp Coordinates

This is both possible and a late answer.

I don't know too much about it, but I believe you can use /execute. This will run the command from the perspective of an entity, so the relative coordinates will be centred on the entity, rather than the source from which the command was run.

Something like this should work, replacing the coordinates and removing the brackets: /execute @p ~ ~ ~ clone (<x1> <y1> <z1>) (<x2> <y2> <z2>) (<x3> <y3> <z3>)

So, for the final set of coordinates (x3,y3 and z3), you can use the ~ to clont relative to the player

Your approach for cloning on a massive scale isn't the best idea. Instead, you should use structures. They can be completely relative to an entity. But going from the idea to move the whole scene, I think it would be better to keep the scene where it is and move the player instead.

So you simply have a command

/tp @p ~0.1 ~ ~

And another command to move a character on the scene (like the bird) and if you want to simulate Flappy Bird, you can now just tp the bird downwards.

/tp @e[tag=bird] ~0.1 ~-0.1 ~

To fly up you can use this command

execute @p[score_jump_min=1] ~ ~ ~ tp @e[tag=bird] ~ ~5 ~

The physics of this wouldn't be perfect, but you get the idea.