I would be careful removing WordPress classes. Some plugins may depend on those classes.
You should be able to pretty easily add your own classes though, as explained in the WordPress Codex. You’d use the nav_menu_css_class
filter to alter or add those classes. See the Codex for an example of doing so. I don’t know what classes twitter bootstrap wants or needs so I can’t really write code for it, and I imagine it would be quite a bit of code anyway to include all the different classes conditionally.
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