I just noticed how long this actually was, so I wil try to answer your question in a shorter way so you can actually get some information out of it.
1: The speed change at the final boss is something to improve the gameplay, but I thought I could do better, so I added a different version of the final boss theme which plays when the speed is changed.
The art style and audio were made in a way I thought it would fit the game and the atmosphere well.
2: I made it every time I took a break, which was when I finished some major element or when I was exhausted. This also meant that I still had in mind how everything was build up and I could make music that would fit the situation.
3: I started working on the story as soon as I chose the main mechanic for the game. I wanted the main mechanic to be a consequence of the beginning, so I had to make it rather early.
4: I wanted it to be a puzzle-platformer with a combat system. There are still a few puzzles, but I realized that I didn't have enough time for more.
5: I'm proud of the polishing because my games are usually very unbalanced, I'm proud of the organized code and a functioning music system, and I'm proud of the overall game and how it was received.