Just to clarify, JuiceboxBuilder is the desktop application which comes with Juicebox to allow you to create and edit galleries on your computer. More information about JuiceboxBuilder can be found here.

As long as you know the location of the images, then you can build the gallery manually following the instructions here. Step #4 is where you would enter each image URL and caption.
Rather than start from scratch with the sample 'web' folder, you could create a gallery using JuiceboxBuilder-Pro (with a couple of sample images) to customize the gallery as you like (using the configuration options on the 'Customize' tab) and then just edit the 'config.xml' file afterwards to change the <image> data.

If you know that all the images for a gallery are going to be in a certain folder, then you could use a server-side scripting language (such as PHP) to dynamically create the required XML file. An example of how this could be achieved can be found in this forum thread.

I do not know how you will be receiving the data but if it is always in the same format, then you could perhaps write a PHP script to convert what you are given into the correct format for a Juicbeox gallery's XML file.

I hope this points you in the right direction.

I'm glad I was able to point you in the right direction.
Incidentally, you could also use DOM techniques to build up a gallery's XML file rather than just echoing the required output. Either would work fine.
If you plan to use PHP and want to use DOM techniques, then the following should get you started. You'll need to create loops for setting configuration options (as attributes to the opening <juiceboxgallery> tag) and for iterating over images (and also extract the relevant data from your source) but this should give you the required structure for a Juicebox gallery's XML file.

<?php
header('Content-Type: application/xml');

$dom_doc = new DOMDocument('1.0', 'UTF-8');
$dom_doc->formatOutput = true;

$settings_tag = $dom_doc->createElement('juiceboxgallery');

// Do this for each configuration option (loop)
// Need to define $key, $value
$settings_tag->setAttribute($key, $value);

// Do this for each image (loop)
// Need to define $image_url, $thumbnail_url, $link_url, $link_target, $image_title, $image_caption
$image_element = $dom_doc->createElement('image');
$image_element->setAttribute('imageURL', $image_url);
$image_element->setAttribute('thumbURL', $thumbnail_url);
$image_element->setAttribute('linkURL', $link_url);
$image_element->setAttribute('linkTarget', $link_target);
$title_element = $dom_doc->createElement('title');
$title_text = $dom_doc->createCDATASection($image_title);
$title_element->appendChild($title_text);
$image_element->appendChild($title_element);
$caption_element = $dom_doc->createElement('caption');
$caption_text = $dom_doc->createCDATASection($image_caption);
$caption_element->appendChild($caption_text);
$image_element->appendChild($caption_element);
$settings_tag->appendChild($image_element);

$dom_doc->appendChild($settings_tag);

echo $dom_doc->saveXML();
?>

I do not know how likely this is to be implemented but I would certainly encourage you to post suggestions for future versions in the Feature Requests thread.
This keeps all the ideas together and ensures that they are not overlooked by the developers. Thank you.

I notice that you have taken the 'juicebox.js' file outside the 'jbcore' folder.
Juicebox needs all the files within the 'jbcore' folder to work correctly (and no files within the 'jbcore' folder should be renamed or moved).
Upload the complete 'jbcore' folder to your web server and load the 'juicebox.js' file from inside the 'jbcore' folder.
This should hopefully solve your problem.