Thomas began taking piano lessons at age eight. He learned major and minor chords and scales and major sevenths and ninths. He had an intuition for putting keys together such that anything he might consider to play would come out beautifully—disguised therein his rote and mechanistic approach to composition. He thought of different note progressions as items in a box, and as he wanted to play something, he would just pull systematically from his box and there was music and it was good. His piano teacher marveled at his acceleration through the levels of adolescent song books. It wasn’t long before Thomas bored of her and asked to stop taking lessons—he had really learned all he needed from her anyway.
But when his parents bought him composition paper to codify ...
But it's all distant and expository. It's information. It is not story.
I could maybe get on board with this - I see the premise you're setting up, but you take too long to get there. The important thing you're trying to show to us isn't what he does with music, but what he does with the composition paper. Get to that sooner. And lose the ellipsis at the end. Too Hardy Boys for me.
And, for the second time this morning, let me say it - spend some time critiquing other people's stories. You'll learn as much as they do, and it keeps this place running.