Very cool.

While I love the look of force-directed-graphs, they wind up representing lots of arbitrary/random values, in all the degrees of freedom of the exact location/angles/proximities they settle into.

I would suggest using a more traditional nested-outline view, either overall or within certain subgraphs. Then, the above/below axis could mean something consistent -- like ordering in source code -- and the left/right something else -- like nesting/composition. And there might be more room for projecting persistent time information -- like a piano roll -- off in a particular direction.

Still very pretty, interesting, and promising!