Some suggestions:
#1. Switch to CoffeeScript. It will cut the size of the code down considerably and given that it is such a massive file, it would really help readability.
#2. Don't embed so much html into the code. That'll also cut down code and make things easier to read. I suggest something like Handlebars to render things. Yes, another dependency, but a good one.
#3. Do you really need the 'please wait' to render things? It is somewhat jarring when clicking around quickly. If anything, just switch the thing you clicked on into a spinner or display a small spinner somewhere.
#4. A lot of the date math that is going on could probably be done more easily by using momentjs. Again, another dependency, but will save you code in the long run.
#5. Grey out buttons which cannot be clicked further? Like the + and - buttons.
#6. Maybe consider integrating or building on top of the Timeline project? http://www.simile-widgets.org/timeline/
Cheers.