Your best bet would be to install MBII manually. Go download this
After it downloads, extract it to its own folder and then move the GameData folder to wherever your Jedi Academy installation is (for example, C:\Program Files (x86)\Steam\steamapps\common\Jedi Academy). Then you need to download this - it's an upgrade from earlier version to the latest version, so that you can play on all the current servers.
Should be as well just a GameData folder or MBII folder that you move to the corresponding folders; that means GameData to \Jedi Academy or MBII folder to \Jedi Academy\GameData