You can get the latest v3.1.1 Bootstrap files from
here. Upload to...
skin/reboot/css/vendor/bootstrap.min.css
skin/reboot/js/vendor/bootstrap.min.js
But I would recommend using the Bootstrap CDN instead of loading from local.
//netdna.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap.min.css
//netdna.bootstrapcdn.com/bootstrap/3.1.1/js/bootstrap.min.js
There is a small bug with BlockUI v20131009 and jQuery 1.10.2. You can revert back to jQuery v1.8.3 without any adverse effects.
//ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js