If you have many galleries uploaded to your web server, you can have them all share a single instance of the 'jbcore' folder by following the instructions here.
When a new version of Juicebox-Pro is released, you need only replace a single folder on your web server to upgrade all your galleries at once.

If you have made any modifications within the 'jbcore' folder (for example to the 'theme.css' file), then these modifications will need to be applied to the new version of the file but since Juicebox-Pro was released, we have added many configuration options (in v1.2.0 and v1.3.0) which can now be set in the gallery's XML file (such as control over shadows and the gallery font) which were previously only achievable by modifying the 'theme.css' file.

This bug has now been fixed in v1.3.2. Please see the Version History for a full list of changes and the Upgrading Juicebox page for details on how to get the latest version.

The issue with the semi-transparent overlay on Android devices has now been fixed in v1.3.2. Please see the Version History for a full list of changes and the Upgrading Juicebox page for details on how to get the latest version.

This bug has now been fixed in v1.3.2. Please see the Version History for a full list of changes and the Upgrading Juicebox page for details on how to get the latest version.

The issue with the semi-transparent overlay on Android devices has now been fixed in v1.3.2. Please see the Version History for a full list of changes and the Upgrading Juicebox page for details on how to get the latest version.

I see the difference in height now. Thank you.
I have notified the developers of this, too.

There is no method to dynamically add images to a gallery after it has initially been loaded.
Each time you add more images to your gallery, you would need to reload the gallery (using the standard JavaScript embedding code). On reloading the gallery, you could use the firstImageIndex configuration option to restart your gallery at an appropriate image.

Yes. This is a known bug which has been addressed and will be fixed in the next version of Juicebox-Pro.
Thank you for reporting.

If you are simply moving your Juicebox-Pro galleries from Domain1 to Domain 2, then there is no need to do anything other than delete all your Juicebox-Pro galleries from Domain1.
A Juicebox-Pro Single-Site license is not tied to a specific domain. As long as all your Juicebox-Pro galleries are uploaded to only one domain at a time, that is fine.

If you wish to have Juicebox-Pro galleries on both Domain1 and Domain2, then please see this FAQ:
Can I upgrade from a single site license to a multi-site license at a later time?

(1) Instead of the following:

new juicebox({
    containerId: 'juicebox-container',
    configUrl: 'ResponseGallery.aspx?id=' + id
    //baseURL: 'http://admin.svstudios.com/App_Upload/',
}).toggleExpand();

... try:

jb = new juicebox({
    containerId: 'juicebox-container',
    configUrl: 'ResponseGallery.aspx?id=' + id
    //baseURL: 'http://admin.svstudios.com/App_Upload/',
});
jb.onInitComplete = function() {
    jb.toggleExpand();
}

(2) I am not sure why you would be getting two responses but perhaps the second one is due to the call to the toggleExpand() method. Try temporarily removing this to see if it makes a difference.

(3) I see the scrolling problem in your web page (on closing a gallery) but have been unable to replicate it in a stripped back test gallery resembling yours as closely as possible (loading the same external JavaScript and CSS files as your page does and using a similar technique to display an expanded gallery from a link on the same page).
Try temporarily removing elements from your web page, one by one, until the problem no longer exists to try to determine the cause of the problem.

Also, it looks like the code:

*
{
    color: #323232;
}

... in your 'main.css' file is overriding the color of the Button Bar icons, the navigation arrow buttons and the titles and captions in your gallery (as the gallery is inheriting this wildcard CSS rule).
You can override this wildcard CSS rule by explicitly setting colors for the elements in your gallery using the available Color Options.

Yes. Set enableDirectLinks="TRUE" (in the 'Customize -> General' secion of JuiceboxBuilder-Pro) and you can link directly to a specific image in your gallery using a URL such as http://www.example.com/gallery/#2
Please see the description of the enableDirectLinks configuration option in the General section of the Config Options page for more information.

First of all, try changing your gallery's background color so that the entire gallery can clearly be seen on your web page.
This should let you know whether the space you are seeing is within the gallery area or elsewhere on your web page.
If the space is within the gallery area, check that you have set both imagePadding and stagePadding to zero.
Also, try setting imageScaleMode="FILL" to ensure that the main image fills the available image area within the gallery. If this removes the space, then it may simply be that the aspect ratio of your main images does not match that of the image area within the gallery and changing the dimensions of the gallery, the shape of your images or the imageScaleMode should help.