Should this be repeated for each of the embeds or is once in the header sufficient?
Loading one instance of the 'juicebox.js' file in the <head> section of your web page is sufficient. (There is no need to load the 'juicebox.js' file for each gallery.)
When looking at the index for gallery1 what is to be placed here? Is it the index.html file at the root of the gallery folder or the full.html file in the jbcore folder?
Under normal circumstances, there should be no need to go into the 'jbcore' folder and the 'full.html' file should be left unmodified in its original location (the root of the 'jbcore' folder). (It is used when going fullscreen in mobile devices.)
Also, the 'index.html' file from a gallery is required only if you want to display the gallery on a page of its own. If you plan to embed the gallery in an existing web page alongside other content, then this file can safely be ignored.
Am I correct that for each slideshow I would need a baseURL for each tab, in my case gingerbread.html and art.html?
If you plan to embed several galleries, then I would recommend the baseURL method of embedding as documented here. This would allow you to upload your complete gallery folders to your web server keeping each gallery separate in its own folder.
The baseURL embedding code should be inserted into your own web page and you should not modify the 'jbcore/full.html' file. (All galleries can safely share a single 'jbcore' folder with the same 'full.html' file.)
As noted above, a gallery's 'index.html' file is required only if you want to display the gallery on a page of its own. It is not required (or used) if you embed the gallery in a web page of your own.
If your gallery does not have a 'full.html' page in the 'jbcore' folder, then your gallery will likely fail when going fullscreen on a mobile device.
Is there a list on your site that includes items that must be in the embed?
Yes. A list of Embed Options can be found here. These options (if used) must be in the embedding code rather than the XML file. All other options can be set either in the embedding code or the XML file. (The exception being debugMode which, if used, must be set in the XML file.)
I noticed that when I only had galleryHeight in the .xml file that it wasn't included in the published page.
The galleryHeight entry in the XML file is not actually used by Juicebox when the gallery is displayed. It is used only by JuiceboxBuilder-Pro to repopulate the fields in the interface when opening an existing gallery to edit it.