If you have the featured pony, the star level of the pony will add 10% to your total score for each star. But if you don't, you'll play with Twilight Sparkle, with no bonus.
When the time runs out, the game is over. To get a high score, it's very important not to miss any time bonus. The yellow clock can appear in about 15 different locations in this game. Each clock you catch gives you nine additional seconds.
There are three clock locations which are quite easy to miss; two of the most difficult to catch are shown below. Once the pony touches the dark clouds, nothing can be caught for 1.5 seconds.
Most Difficult Location 1A pony needs to fly extremely accurately, touch the clock then quickly return above to avoid touching any dark clouds.
A small filly needs to run on the ground until she is just under the clock. The dark clouds can be avoided since a filly is not tall enough to touch them.
Most Difficult Location 2
Clocks can randomly appear in the background and easily be overlooked. Watch for them CAREFULLY!