you may want to use a local server for testing, python for example. Then I'd go trough all scripts an remove external dependencies, DL those scripts and host them locally. I wonder what you need JQuery for...
It's hard to say what's wrong without to know the program structure. Is it using SetTimeout() in JS to execute a "mainloop", or ist it something completely unrelated, like a text adventure in HTML? Anyway, if it is framebuffer oriented, try using the system milliseconds counter to locate the part of the code that slows things down.
edit: you said you're using DIV tags to show and remove elements. I hope you don't create and delete HTML-elements, but instead simply hide them by css attribute display="none".