Hi.

If you want to remove support for earlier versions of IE, you could remove all CSS rules relating to the following classes from the 'theme.css' file:
.jb-flag-msie-bf9 (rules relating to all versions prior to IE9)
.jb-flag-msiever8 (rules specific to IE8)
.jb-flag-msiever7 (rules specific to IE7)

If you really wanted to remove support for all versions of IE, you could remove all CSS rules relating to all classes starting with:
.jb-flag-msie

Unfortunately, you won't be able to do similarly for the 'juicebox.js' file as it is compressed and packed/obfuscated and so cannot be modified.
(Also, as noted in this FAQ, modifying the source code is not supported.)

Even if you could modify the 'juicebox.js file, removing the built-in version of jQuery would not be a trivial matter.
You'd need to make sure that all remaining JavaScript code is compatible with whatever version of jQuery you plan to include in your page (checking for the presence of deprecated and removed  functions).
Also, there's surprisingly little JavaScript code relating specifically to IE and removing it would probably only save you 2 or 3 kilobytes from the overall size of the file.
Removing jQuery would obviously reduce the size of the JavaScript file more considerably but it's just not possible for a user to do.