No. Such modifications (using internal CSS classes and custom JavaScript) are not officially supported (but you can use them at your own risk).
We support the use of the available Config Options and make available the Juicebox-Pro API, but even the API has limited official support, as noted on the API's support page:

Sometimes, users request things that are just not possible using the available Config Options and/or the API.
I'm happy to try to provide a solution if I can but sometimes the solution requires some custom code (CSS and/or JavaScript).
Such modifications are not officially supported as there are far too many possible permutations to document/list and using such modifications can often result in unforeseen and unwanted knock-on problems.
One small and seemingly easy request may snowball out of control into a complex coding mess and it's much safer to stick to the available Configuration Options where possible. If you modify a gallery beyond what is possible with the Config Options, Juicebox will have no knowledge of the modifications and this can quite often cause problems (when Juicebox expects something to happen or a gallery element to be in a certain location and this is not the case due to the modifications).
Also, I really have no greater insight into the inner CSS classes of Juicebox than you do.
I just have to rifle through the 'theme.css' file and use my browser's developer tools to try to figure out how to achieve something (like the code I've posted above).
Having said that, you are certainly free to do whatever you like with Juicebox and your web pages (within the Terms of Use and without modifying the 'juicebox.js' JavaScript source code) but just remember that, if you go beyond the Config Options, then you might run into problems that can be difficult to overcome.

That's great! Thank you for letting me know.

It's probably just that your gallery is too tall and that the images cannot be scaled any larger within the gallery without being cropped at the left and right sides (which you could try by setting imageScaleMode="FILL").
Hopefully reducing your gallery's height will help to minimize the space between the images and thumbnails.

You're welcome!

It looks like you should set z-index: 9999; on your .header CSS class.

<style type="text/css">
    .header {
        z-index: 9999;
    }
</style>

This should hopefully solve your problem.

No, at least not directly.
The thumbnails are positioned via the thumbsPosition configuration option and the main images within the gallery are dynamically scaled (within the gallery's image area) via the imageScaleMode configuration option. As such, there is no configuration option available to simply adjust the distance between the thumbnails and the main images.
If you want to reduce the space between the thumbnails and the main images, then try reducing the height of your gallery slightly. (Try a fixed height of '600px' or '800px' initially and see how things look.) The same vertical space as before will be reserved for the thumbnails so, reducing the height of your gallery will result in less height being available for the gallery's image area and there should be less space above and below the main images.
Please see this FAQ for further details.
My Juicebox gallery shows too much space above or below the main image, how do I fix this?

I hope this helps.

As long as your 'Birds' directory is a complete gallery folder, then there should have been no need to change any of the paths in the code I posted above. The leading slashes denote your root directory and avoid the need to use absolute paths or calculate relative paths.

When using the baseUrl method of embedding, the gallery's configuration file should be named 'config.xml' and should be located directly inside the gallery folder. If you move or rename the XML file, then you can point towards it with a configUrl entry in your embedding code.
However, your 'Birds' gallery folder seems to include a 'config.xml' file (named and located correctly: http://www.sieg.be/Birds/config.xml) so the code I posted above should have worked fine without modification.

Try using the embedding code I posted above again.
If you continue to experience difficulties, then please post the URL to your gallery's web page so that I can see the problem for myself and hopefully help further.
Once I'm able to see your gallery live on your web server, I should hopefully be able to determine the exact cause of the problem and propose a solution.

In the meantime, please check out this FAQ which might also help.
When I view my gallery I see the message 'Config file not found'. How do I fix this?

If your 'Birds' directory is a complete gallery folder, then you can use the baseUrl method of embedding documented here.
You can use the following embedding code to embed your 'Birds' gallery into a web page.

<!--START JUICEBOX EMBED-->
<script src="/Birds/jbcore/juicebox.js"></script>
<script>
    new juicebox({
        baseUrl: "/Birds/",
        containerId: "juicebox-container",
        galleryWidth: "800",
        galleryHeight: "600",
        backgroundColor: "#222222"
    });
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

The leading slashes in the paths above denote your root directory so the code above will work in any web page throughout your website without modification.

I would recommend that you embed your gallery directly into a web page (like in the example above) as there are drawbacks to using an iframe. Please see here for details (scroll down to "2) Using an iframe").
However, if you really want to load your gallery into an iframe, upload the complete gallery folder (including the gallery's 'index.html' file) to your website and load the gallery's 'index.html' file into your iframe (i.e. use the path to the gallery's 'index.html' file as the 'src' attribute in your iframe).
The 'index.html' file appears to be missing from your 'Birds' directory at the moment (or has permissions that are currently too restrictive), but, assuming it is there and readable, you could use an iframe such as:

<iframe src="/Birds/index.html" width="800" height="600" frameborder="0" scrolling="no"></iframe>

I hope this helps.

captionBackTopColor is actually the only configuration option which has different default values for Large Screen Mode (rgba(0,0,0,0)) and Small Screen Mode (rgba(0,0,0,0.3)) so if you do not change captionBackTopColor in JuiceboxBuilder-Pro's interface, a captionBackTopColor value will not be written to the gallery's configuration file and the two default values will be used (which, when combined with the default value for captionBackColor, gives a gradient background in Large Screen Mode and a solid background in Small Screen Mode).

If you want to ensure that a single captionBackTopColor is used in both screen modes, then change its color or opacity slightly from its default value. This will ensure that a captionBackTopColor entry is written to the gallery's 'config.xml' file and the chosen value will be used in both Large Screen Mode and Small Screen Mode. Then, to remove the gradient, set captionTopColor to exactly the same color and opacity as you've used for captionBackTopColor.

First of all, if you have any security software installed (e.g. Avast, AVG, etc.), please make sure that the program itself and its database are both up to date.
If this does not help, then try completely disabling your security software (at your own risk) or make an exception for the JuiceboxBuilder executable file to see if this makes a difference.
We've had a couple of Avast users report similar symptoms to those that you describe. However, I contacted Avast and they say that they cannot replicate the problem with the latest version of their software (v18.3).

If this does not help, then, with JuiceboxBuilder-Pro closed, please check to see if the following folder exists on your system:

C:\Users\Username\Documents\JuiceboxBuilder-Pro\.tempGallery

If there is a .tempGallery folder in this location, please delete it manually.

The .tempGallery folder is created automatically by JuiceboxBuilder for internal use only (for the live preview window and as a temporary gallery folder until the gallery is saved on the 'Publish' tab).
It should automatically be deleted by JuiceboxBuilder-Pro on closing the application but, if this fails, it has been known to render the 'New Gallery...' and 'Open Gallery...' buttons inactive.

The only way that I've been able to replicate the symptoms that you describe myself is to save a gallery to a Google Drive folder (so I'd recommend not saving a gallery to a location which is being synced to an online file sharing service) and the problem seems to be due to a persistent .tempGallery folder (which has not been removed as expected).
You may not be using a Google Drive folder but a persistent .tempGallery folder might still be causing a similar problem.

Hopefully my notes above will help.

Each gallery must have a unique 'config.xml' file which stores the gallery's configuration options and image data, but there is no need to keep each gallery self-contained in an individual folder (although it can certainly help to keep things organized on your web server). You can point towards a gallery's 'config.xml' file (in any location you like) using a configUrl entry in the gallery's embedding code.

The only file within the 'jbcore' folder which may change from gallery to gallery is the 'pswd.php' file which contains the password for a gallery (if you choose to password-protect it).
Please see the Password Protection support section for details.

If you do not want to password-protect your galleries (or if you are happy to use the same password for all your galleries), then all your galleries can share a single instance of the 'jbcore' folder (rather than having an individual 'jbcore' folder for each gallery).
If you'd like to do this, then please see the Using an External jbcore Folder support section for details.

Essentially, all you need to do is upload a single 'jbcore' folder to somewhere on your web server and make sure that the 'juicebox.js file (from within the 'jbcore' folder) is loaded via a <script> tag on every web page which contains a gallery.

If all your galleries share a single instance of the 'jbcore' folder, then you can upgrade all your galleries at once (for example, when a new version of Juicebox-Pro is released) simply by swapping your single 'jbcore' folder for a new version.

Open the template file that JuiceboxBuilder-Pro uses to generate the gallery's 'index.html' file and change the <title> there (so that your custom text appears as the <title> in all 'index.html' pages generated by JuiceboxBuilder-Pro).

Open the following file in a plain text editor:
Mac: /Applications/JuiceboxBuilder-Pro.app/Contents/Resources/template/index.html
Windows: C:\Program Files (x86)\JuiceboxBuilder-Pro\template\index.html

Now, scroll down to line 4 and change:

<title>%%TITLE%%</title>

... to:

<title>Tony Gamble Photography</title>

The text displayed in the browser tab comes from the contents of the <title> ... </title> tag (in the <head> section of your web page).

If you create a gallery with JuiceboxBuilder-Pro, then the application uses the Gallery Title for the <title> tag in the gallery's 'index.html' file.

However, you can open any HTML web page in a plain text editor and manually edit the page's <title> to whatever you like.
Just search for "<title>" (there should be only one entry in each web page) and change the text between the opening and closing <title> and closing </title>.

I'm glad you've got it working! Thank you for letting me know.

Incidentally, there should have been no need to delete any data within WP-Juicebox.
All you need to do to upgrade the plugin from Juicebox-Lite to Juicebox-Pro is to replace the plugin's Lite 'jbcore' folder with the Pro version from the Juicebox-Pro v1.5.1 download zip package ('juicebox_pro_1.5.1/web/jbcore').
You can do this before or after the plugin has been uploaded to your web server.

You could actually swap out the entire plugin (which you might do when the plugin is updated) without affecting any galleries or plugin settings. No custom data is stored within the plugin's directory. All custom gallery settings are stored in XML files in the 'wp-content/uploads/juicebox/' directory and all custom plugin settings are stored in the WordPress database.