It looks like it may be possible to implement this for a website containing a Juicebox gallery but it does not look like something that can be integrated within Juicebox itself (as it requires, amongst other things, creating HTML snapshots).
(As you are already aware, it would also require implementing a new direct linking technique as Juicebox natively uses # rather than #!.)

When creating a Juicebox gallery, you have the choice to name the Index Page Name on the Publish tab.
If you save each gallery to a different folder (which I would recommend) you can safely leave the Index Page Name as the default value of 'index.html'.
No new files are created whilst uploading your gallery. Uploading is simply a process of copying files and folders from one location( your computer) to another (your web server).
(As you are embedding your galleries in other web pages, you do not actually need any of the 'index.html' files. They are used only when you wish to view the galleries on pages of their own.)

That sounds like the reason that your galleries do not function correctly.
Just leave the gallery folders exactly as they are created by JuiceboxBuilder-Lite and upload them in their entirety.

If you upload a complete gallery folder named 'gallery2' to the root of your web space (exactly as it is created by JuiceboxBuilder-Lite) and use the following embedding code in your http://www.finecustombuilding.com/exteriors.html file, the gallery will display on the page.

<script src="http://www.finecustombuilding.com/gallery2/jbcore/juicebox.js"></script>
<script>
  new juicebox({
    baseUrl : 'http://www.finecustombuilding.com/gallery2/',
    containerId : 'juicebox-container2',
    galleryWidth : '930px',
    galleryHeight : '700px',
    backgroundColor: '#222222'
  });
  </script>
<div id="juicebox-container2">

The 'config.xml' file is located inside each gallery folder (alongside the 'index.html' file and 'images', 'thumbs' and 'jbcore' folders).

Current problem with 'Exteriors' gallery:
The path to the 'juicebox.js' file is incorrect.
Change:

<script src="http://www.finecustombuilding.com/gallery2/images/jbcore/juicebox.js"></script>

... to:

<script src="http://www.finecustombuilding.com/gallery2/jbcore/juicebox.js"></script>

Going to the first image in your Exteriors gallery (http://www.finecustombuilding.com/galle … erior1.jpg) directly in a browser does not display the image as expected.
Things to check:
(1) Double-check that the file actually exists in the correct location.
(2) Make sure that the file extension of the imageURL entry in your gallery's XML file matches that of the image itself. Your web server is likely to be case-sensitive and .jpg is not the same as .JPG.
(3) Check the permissions on the 'images' folder (and the images themselves) to ensure that they can be read.

It looks like the 'jbcore' folder is missing from your 'gallery3' directory on your web server.

Whether you upload the files via Dreamweaver or a separate FTP program, you would need to ensure that the contents of the gallery folder (not the folder itself) are in the root of your web space so that, for example, your gallery's XML file (named 'config.xml') is located at www.cdstiling.co.uk/config.xml

The Juicebox embedding guide can be found here.
There is also a note for Dreamweaver users here.
However, as I mentioned before, if you plan to embed multiple galleries, I would recommend using the baseUrl method of embedding as documented here.

Essentially:
(1) Upload your complete gallery folder (in this example, named 'mygallery') to the root of your web space (depending on your web server this is likely to be a folder named 'public_html' or 'htdocs').
(2) Change your current embedding code to the following:

<!--START JUICEBOX EMBED-->
<script src="http://www.cdstiling.co.uk/mygallery/jbcore/juicebox.js"></script>
<script>
new juicebox({
baseUrl: "http://www.cdstiling.co.uk/mygallery/",
containerId: "juicebox-container",
galleryWidth: "100%",
galleryHeight: "600",
backgroundColor: "#222222"
});
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

Just to clarify, I do not know if the developers will implement your suggestion but you have posted your feature request in the correct place and it will not be overlooked.
Hopefully you will be able to implement one of the suggestions in my previous post to achieve the functionality you require.

Thank you for providing the URL to your web site.
As you are embedding only one gallery per web page, there is no need to name your container ids differently (although it will do no harm) as there will be only one gallery container per page and there will be no conflict with any others.

Currently, the problem with your 'Interiors' gallery is that your http://www.finecustombuilding.com/interiors.html page contains the line:

<script src="http://www.finecustombuilding.com/gallery1/jbcore/juicebox.js"></script>

... but the 'juicebox.js' file does not seem to have been uploaded to that location.

I would start by embedding the galleries first and only then, once everything is working as required, would I recommend having your galleries share a 'jbcore' folder.

Essentially, just follow the baseUrl embedding instructions here for one gallery and, once you have got one working, move onto the next.

Upload a complete gallery folder, named 'gallery1' to the root of your web space and that gallery should be displayed on your 'Interiors' page (as the embedding code itself on the http://www.finecustombuilding.com/interiors.html page looks OK).

With Juicebox-Pro (though not with Juicebox-Lite), you would be able to set showSplashPage="NEVER" to skip the Splash Page and initially display the first image in the gallery. Alternatively, you could also set screenMode="LARGE" to force Juicebox-Pro to use Large Screen Mode on all devices and in all browsers. For more information on Screen Modes, please see here.

I have viewed your gallery on my iPod Touch and your gallery displays OK. I do not see the 'Config XML not found.' error message.
Try clearing your browser's cache before reloading the gallery to make sure that your browser does is not hanging onto and using older versions of your gallery files.

Thank you for posting your suggestion in the Feature Requests thread.

As well as the AutoPlay button on the Button Bar (which can be displayed by setting showAutoPlayButton="TRUE" in your gallery's XML file), you can also toggle the AutoPlay status on and off programmatically using the toggleAutoPlay() Juicebox-Pro API method.

@alelia

Thank you for the suggestion.

As well as the AutoPlay button on the Button Bar (which can be displayed by setting showAutoPlayButton="TRUE" in your gallery's XML file), you can also toggle the AutoPlay status on and off programmatically using the toggleAutoPlay() Juicebox-Pro API method.

Please take a look at this forum thread for a Juicebox adaptaption of the SEO Script I linked to in my previous post above.

With regard to your latest query, you could set enableDirectLinks="TRUE" in your gallery's XML file (which will give each image a unique URL using the '#' character) and you could then use the onImageChange() Juicebox API event to add SEO code to a container (which would be hidden via CSS) using JavaScript. However, I do not know how Google would treat this. There would essentially be only one page and Google would not know how many dynamic versions of the page could be created by appending image numbers to the URL.

@ZabParis

If you were to load the gallery into an iframe, display the page containing the iframe in a browser and view the source of the iframe, then the SEO code will be displayed.
However, if you would like the SEO code to be inserted into the page which contains the iframe, then you would need to create a container on the page with the iframe, such as:

<div id="seo"><?php include("juicebox-seo.php"); ?></div>

... and hide it with CSS such as:

<style type="text/css">
    #seo {
        display: none;
    }
</style>

If you would like your gallery's height to be 600px, then, rather than using:

#juicebox-container {
    width: 100%;
    height: 600px;
}

<script>
    new juicebox({
    containerId : 'juicebox-container',
    galleryWidth: '100%',
    galleryHeight: '100%',
    backgroundColor: '#222222'
    });
</script>
<div id="juicebox-container"></div>

... just set the gallery's height in the embedding code:

<script>
    new juicebox({
    containerId : 'juicebox-container',
    galleryWidth: '100%',
    galleryHeight: '600',
    backgroundColor: '#222222'
    });
</script>
<div id="juicebox-container"></div>

Also, if you would like to have a header on your web page and then have your Juicebox-Pro gallery fill the remainder of the user's browser window (with no vertical scroll bars), please see the Using a Resizable Gallery with a Header example in the Juicebox Embedding Guide.