Woooohooooo! It works!!!
All of the embed options can be used in either the embed code or config.xml. I should have realized this, a bit short sighted of me, but still new with JB pro.

One config.xml file. I don't even need separate gallery folders, just embed code in gallery pages (joomla articles). One folder for jbcore, one config.xml, all the unique data in the embed code. This is awesome. Even with some of the rough edges and features I would like to have, this is better than any of the other Joomla gallery components we looked at to replace Slideshow Pro. I think I might even create a Joomla Juicebox component. It's very straight forward.

Next I am going to use gor555's trick to create embed code using the html template. I am not using the standalone html template, and won't ever use it within our workflow, but I can simply modify it so it produces JUST the embed code for each gallery. I have to modify each chunk of embed code anyway, I can truncate the html so it's only a "code snippet" to be copied and pasted.

Okay I found what I thought is the html template and modified it, but the embed code in the application does not change.

It's the same as it was before, with the default settings on the Publish screen of Juicebox builder.
I want to add and change options to the embed code "template" so I don't have to edit it every time after saving.

I want to add the base url option to the embed code using %%TITLE%% and also change the location of the jbcore.

"sidmiller" is the title or name of the gallery:

baseUrl: 'galleries/sidmiller/'

On the Publish screen there is a text box to copy the embed code.
Modifying the index.html template in the application does not change the embed code when creating a new gallery.

This is what I want the embed code to look like

<!--START JUICEBOX EMBED-->
<script src="galleries/jbcore/juicebox.js"></script>
<script>
new juicebox({
containerId: "juicebox-container",
baseUrl: 'galleries/sidmiller/',
galleryWidth: "100%",
galleryHeight: "80%",
backgroundColor: "rgba(255,255,255,0)"
});
</script>

Another thing I am looking for if possible, is to edit the config.xml "template".
Is there a file in the application that controls any of the output for the config.xml?
I am changing elements in this file as well.

I need the XML on the live site. As has been mentioned before, this file contains paths of the local system. I edit config.xml sourcePath to point to a local folder using a relative URL instead of the full path with all of my computer folder information.

I don't want a file on the website with that type of information of my work computer. I would like to remove it by default instead of having to edit files.

It seems there's a lot more "hands on" editing of embed and config in a text editor. Just curious why these changes can't be implemented in the Juicebox builder application to avoid extra work and eliminate "user error" mistakes, like... twice I uploaded galleries but forgot to edit the embed I pasted in.

I would really like that embed code to be "done" on save rather than having to edit it.

Thanks for the response!

Actually I did a simple css override of that class and it works PERFECTLY. Normally I hate to override inline css but in this case it was so simple and fast it seemed the best solution.

I did same thing you posted, changed that class to z-index: 400 !important;. Works fine, no other unusual results. A further note on this... there really is nothing I can see that would require a 3000 z-index. It is such an outrageous value. Even within the DOM of the embedded slideshow there isn't anything in there that would account for 2999 other elements. :)

On second thought, the 400 z-index was based on getting the button bar to float over everything just IN THE GALLERY CODE. To float over the site navigation could have been much lower. Anything LESS than 400 and the button bar could not be clicked. I think this is why it is set so high. The JS generated inline css is just using a REALLY HIGH value in case someone has a gallery with 2999 images. :) Since none of my galleries currently are more than 100 images that value works. I may have to bump it up later of course.

I think this is because of the absolute positioning of the button bar. If it were relative to everything else, I think it would not float over the outer, separate header, navigation. Not 100% sure but pretty sure that relative z-index only works within that block.

p.s. I did set the z-index of the header and navigation of the site template to a pretty high value just to "get it out of the way" so to speak. There were other components and "gizmos" that kept floating over the navigation. The header and navigation is "animated" and "fixed" as you scroll it shrinks and stays at the top.

Tag Filter Feature

This was covered in a previous response to the same request, suggesting using an image hosting site such as "Flickr" I think, tagging images there and filter with links in Juicebox.

But I'm going to request again that "tag" filters would be a great feature in the core gallery, rather than linking to some other image gallery website. I would be interested in even something very very very very basic, doesn't even need to be fully fleshed out, would be willing to do any design or coding to access tags within each image. Maybe some sort of "hybrid" solution using the same filtering avaiable with externally provideed images.