Is it permissible to file down the protruding part of the second molar so that it is level with the other molar, knowing that this filing is very minor, and does this fall under altering Allah's creation or being among those who widen gaps between their teeth for beauty?

It is permissible to file down teeth and molars to equalize their length if the unevenness causes harm. However, it is not permissible to do so for the sake of beauty, based on the hadith of Ibn Mas'ud (may Allah be pleased with him), which curses those who create spaces between their teeth for beauty, because it is an alteration of Allah's creation. Therefore, if the length of a tooth causes difficulty in eating or speaking, it is permissible to file it down; otherwise, it is not. You have done well in stopping the circular filing of molars, as it falls under the prohibited categories of washr (sharpening teeth) and tafalluj (creating gaps between teeth).