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I assume that you put the batch file on the USB stick? It expects the folders it refers to to be relative to the location of the batch file.
When you copied the calibre2 folder onto the USB stick did you keep that name (you implied that you did)? If so then change the references in the batch file to CalibreBinaries to be calibre2 instead (or rename the calibre2 folder on the USB stick to be called CalibreBinaries to match the batch file)
Do not worry about the CalibreConfig folder being empty, it will be automatically populated by Calibre as you set your preferences in Calibre. You would have an equivalent folder called 'calibre' somewhere in your user profile, but as long as you are prepared to start with default settings for preferences then you might as well start with the CalibreConfig folder being empty. It is important that your preferences are stored in this folder as otherwise they would be stored locally on each machine which means they would not follow you as the USB stick is moved around.
The batch file has a Pause command in it just before attempting to Start Calibre and it displays the settings that are about to be used. You should check that these correspond to the folder names on the USB stick before proceeding to try and load Calibre.
Hope this description helps?
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