Hello, Stephen
Although still under initial development, you may want to look into the visualization registry for the infrastructure to render the region and allow the user to interact with it:
In a nutshell, it allows you to configure and include a link from the history panel to a custom page that you create with the mako templating system and the javascript you'll need for the interactivity. Galaxy resources (like your initial dataset) are parsed for you and available in the template.
For the other half of the problem: creating new data from the interaction of the user, you'll want to look into the tools API (which is what Trackster uses). Still somewhat rough, there have been improvements to it lately that should allow you to run a tool based on user input and keep the chain of reproducibility.
Two things to note:
1. I'd recommend not using the upload tool via the API: not because it doesn't work but because adding arbitrary data this way won't be reproducible.
2. Both the visualizations registry and the tools API are still under development. Feel free to contact me on IRC, email, or the mailing lists if you have any trouble though.
I hope that helps and let me know if I can provide any more information,
Carl