A Molecular clock would be gravity in your model, when ever you called stop all your marbles would have experienced the same amount of gravitational force. That is the intent of "experienced the same amount of evolution" and similar.

Where I see the model flounder is; the hill provides the fitness context. You implied distance "means" more evolved, but for life it is all about making it to the next round, in your marble game how many of those furthest marbles will ever be found for the next round?

With life big changes are dangerous, you may find yourself improved out of options.