Yes (although this should not be necessary).
What you are describing is actually a known bug whereby elements which have explicitly been assigned a CSS 'position' are not covered when the gallery is expanded either from the Splash Page or by clicking the Expand Button (they should be). This bug has already been addressed and will be fixed in the next version of Juicebox (although I do not know when it will be released).
In the meantime, the workaround (for Juicebox-Pro users), is to set expandInNewPage="TRUE" so that, when the gallery is expanded, it is displayed on a page of its own rather than on top of the embedding page.

Each user will have different requirements and, in resizing images, it may help to know the target audience.
For example, if your gallery is likely to be viewed on a mobile device, then you could probably get away with having much smaller images in your gallery than if the gallery is likely to be displayed on a large desktop monitor (the content of the images and web site may play a part in determining this).
The default values in JuiceboxBuidler-Pro usually result in a good compromise between size and quality for most users (or at least a good starting point for the values to be tweaked).

Personally, I convert my own RAW images to JPEG and then feed these JPEG images to JuiceboxBuilder.
The source JPEG images are approximately 10MB each and, using the default 'Large Images' settings of 2048 x 1536 at 80%, the resulting large images are approximately 400KB each. The resulting image look good enough for me (although I understand that everyone will have their own opinion as to what is 'good enough' for their own galleries).

I do not know exactly how JuiceboxBuilder-Pro internally resizes PNG images (using whatever resizing library or algorithm that Adobe AIR provides) but the only user controls are the dimensions and quality settings.
It looks like you would have much smaller (file size) images if you worked with JPEG images from start to finish.

As long as your source images are of a high enough quality, it is unlikely that the images used in your gallery would be visually unacceptable (especially if you kept the quality setting high enough).

Otherwise, you could always create your own set of large images in Photoshop and copy them across into your gallery's 'images/large/' folder. It might be an extra step in your workflow but if it results in a gallery that you are more happy with, then it might be worth doing.

The z-index value of your menu should be higher than that of your gallery (and its internal components) so that the menu is stacked on top of the gallery. I would recommend trying a z-index value of 9999 for your menu (and not manually applying a z-index value to any gallery elements at all).

Also, you will need to ensure that the z-index value is assigned to the correct class or id of your menu system.

If you are unsure which classes or ids should be assigned z-index values, please post the URL to your web page so that I can take a look and hopefully help further.

It's not so much Juicebox that doesn't understand src=„juicebox/jbcore/juicebox.js" but your browser.
RapidWeaver may be escaping the initial double quote in order to display the actual embedding code as text on your web page.
Please make sure that you are entering your embedding code as HTML code rather than plain text.

Incidentally, „ is a double low-9 quotation mark. You should probably be using standard double quotation marks (which would escape to ") instead.

Please post the URL to your gallery's web page so that I can take a look and help further. The problem is likely to be the path to the gallery's XML file.

Again, ensuring that you are entering your embedding code as HTML code rather than plain text should hopefully solve this problem. Chapter 7 in this web page may help with this.

The 'theme.css' file which comes bundled with Juicebox-Pro v1.4.2 is the correct one (even though it is labelled as v1.4.1).
The labelling of the file as v1.4.1 was just an oversight (it should have been labelled as v1.4.2).
v1.4.1 and v1.4.2 actually use the same 'theme.css' file.

The only change in Juicebox from v1.4.1 to v1.4.2 was the handling of Flickr API URLs (please see the Version History for full details of changes between versions) and this did not require any CSS changes.

I hope this helps explain things and reassures you that the 'theme.css' file in v1.4.2 is OK.

Unfortunately, there will inevitably be unforeseen pitfalls when trying to make Juicebox do something it was not designed to do (especially when interacting directly with Juicebox CSS classes).

Perhaps the easiest way to overcome this problem might be to give your gallery fixed pixel dimensions (rather than percentage dimensions) so that the gallery is not resized dynamically if/when the browser window is resized.

The Button Bar should certainly appear when buttonBarPosition="TOP". Make sure that the topAreaHeight (in JuiceboxBuilder-Pro's 'Cusrtomize -> General' section) is not too small for the Button Bar to be visible.
The Open Image button will always be part of the Button Bar and the Button Bar can be positioned only using the buttonBarPosition configuration option (OVERLAY, OVERLAY_IMAGE, TOP or NONE).

It sounds like setting buttonBarPosition="TOP" and buttonBarHAlign="LEFT" (to horizontally align the Button Bar to the left side of the gallery) might be suitable for your gallery's layout.

Alternatively, you could create your own HTML 'Open Image' button, position it on your web page alongside your gallery and have it act like the Juicebox 'Open Image' button by opening the main image in a new tab or window when it is clicked.
You would use the Juicebox-Pro API (specifically the getImageInfo() method) to determine the imageURL (or linkURL) of the currently displayed image and then use JavaScript to open the URL in a new tab or window.

If you would like to see how a custom 'Open Image' button would work, then create a sample gallery using JuiceboxBuilder-Pro and use the following code as the gallery's HTML index page.

<!DOCTYPE html>
<html lang="en">
    <head>
        <meta charset="utf-8" />
        <meta name="viewport" id="jb-viewport" content="minimal-ui" />
        <style type="text/css">
            body {
                margin: 0px;
            }
        </style>
        <script type="text/javascript" src="jbcore/juicebox.js"></script>
        <script type="text/javascript">
            var jb = new juicebox({
                containerId: "juicebox-container",
                galleryHeight: "400",
                galleryWidth: "600"
            });
            $(document).ready(function() {
                $('#open').click(function() {
                    var index = jb.getImageIndex();
                    var info = jb.getImageInfo(index);
                    var url = info.imageURL;
                    window.open(url);
                });
            });
        </script>
        <title>Test</title>
    </head>
    <body>
        <div id="input">
            <input id="open" type="button" value="Open Image" />
        </div>
        <div id="juicebox-container"></div>
    </body>
</html>

If you continue to experience difficulties, please post the URL to your gallery's web page so that I can take a look and help further.

Please note that we did not write the Juicebox module for Drupal ourselves and I am not familiar with its code (or how it populates the image titles and captions).
Other Drupal users may be reading this thread and can perhaps contribute some useful information but you would likely receive more help by posting your query in the Drupal forum where the author of the module will be able to answer your query.

With regard to the Image Field Caption, the documentation on this web page says the following:

Please check that you have the Image Field Caption module enabled. This might be the cause of your problem.

I realise that this may not directly answer your query but I hope it at least points you in the right direction.

I'll try to break it down for you by commenting the code.

<!--START JUICEBOX EMBED-->
<script src="jbcore/juicebox.js"></script>
<script>
    // Need to give 'juicebox' object a variable name (e.g. 'jb') so that you can refer to it later.
    var jb = new juicebox({
        containerId: 'juicebox-container'
    });
    // onImageChange function is fired each time a different image is selected.
    jb.onImageChange = function() {
        // If the selected image is the first one...
        if (jb.getImageIndex() === 1) {
            // Standard JavaScript timeout is required to work correctly. Need to wait a short while before image can be replaced.
            setTimeout(function() {
                // The next line uses jQuery (bundled within the 'juicebox.js' file) to replace the main image (class name 'jb-dt-main-image') with custom HTML code.
                $('.jb-dt-main-image').html('<p>Text to be displayed in place of the first image.</p>');
            }, 250);
        }
    };
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

I hope that makes it a little more understandable.
Essentially, you would give your 'juicebox' object a variable name (such as 'jb') and add the following code to your gallery's web page (below the gallery's embedding code), changing the HTML text as appropriate:

<script>
    jb.onImageChange = function() {
        if (jb.getImageIndex() === 1) {
            setTimeout(function() {
                $('.jb-dt-main-image').html('<p>Text to be displayed in place of the first image.</p>');
            }, 250);
        }
    };
</script>

I hope that helps.

I understand your concerns and requirements but, unfortunately, I cannot answer your questions directly as I am not the author of Juicebox and I did not make any of the design decisions. I hope you understand.
However, thank you for posting your suggestion in the Feature Requests thread.

Juicebox-Pro does not have a configuration option similar to SimpleViewer-Pro's imageNavStyle="CURSOR".
However, being that Juicebox is an HTML gallery, you could create your own 'previous' and 'next' navigation cursors and apply them via CSS to the 'left' and 'right' hit areas of the gallery using the following classes.

.jbn-nav-touch-area.jbn-nav-left-touch-area {
    cursor: url(previous.cur),auto;
}

.jbn-nav-touch-area.jbn-nav-right-touch-area {
    cursor: url(next.cur),auto;
}

For more information on the CSS cursor property, please see here.
You could create custom cursors using this online cursor editor.

You can selectively load a specific XML file using JavaScript and the configURL option as follows:

<!--START JUICEBOX EMBED-->
<script src="jbcore/juicebox.js"></script>
<script>
    var config = 'spanish.xml';

    if (language === 'english') {
        config = 'english.xml';
    }
    
    new juicebox({
        configUrl: config,
        containerId : "juicebox-container",
        galleryWidth: "100%",
        galleryHeight: "100%",
        backgroundColor: "#222222"
    });
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

In the example above, you would need to define your own 'language' variable and test it to determine which XML file to use.