I'm going to guess that your plastic sunroof gears might be broken, or, the arms were not aligned correctly after installing new gears.

Here is what I would do to fix your problem.

Close the sunroof all the way and remove the sunroof from the car.

Remove the large cover from underneath the sunroof arms. Then remove one of the small covers from the sunroof arm. After removing this small plastic cover the arm, and gear should fall out. Check the gear to see if any teeth are missing. If no teeth are missing, then check the other arm and gear. If no teeth are missing then all you need to do is realign the arms.

To align the arms: Remove both arms and both gears. Now check to see if your sunroof cam is broken. I've attached a picture to show what a broken cam looks like. If you see the cable sticking out, like in the picture, then your cam is brokens and you will need to fix this before moving on. (we sell and aluminum one) If the cam is not broken, (key on to acc.) then push the button to close the sunroof all the way. Keep the button pressed until the cable stops moving. Now you can insert the plastic gears and the arms. Install the arms in the fully closed position on both sides. And install the small cover that holds the arms and gears in.

Now test out the sunroof by reinstalling it and checking to see how high it opens.

If the plastic gears are broken you will need to replace them first. But before replacing them you will need to adjust the sunroof motor clutch. They become too tight over time and that's what causes the broken sunroof gears. It's an easy fix.