So, are we allowed to go in and fix up some of the things that could aide in the flow of the game?

For example, I would like to add a button and a menu option on the main screen to explain game play better. I would also like to clean up the boss battle a bit, and the end game screens. I wouldn't change the game play, or the theme, I would just clean it up a bit. I have about 600 lines of code that could use a bit of refactoring.

Is that allowed?