You can easily edit the basic PDFE Web interface html template files, present at the "WebServ" sub-folder where PDF Explorer is installed, usually "C:\Program Files\PDF Explorer\WebServ".
You only need to maintain the html filenames, and its non-standard html tags (and, in some cases, these tags nested hierarchy). You need to keep also the var strings of the type %SomeIdStr% used, mostly, to enable text language translations insertions, but also to present search variables.
Also, if you need to use additional resource files (images, css, javascript,...), place them inside that WebServ folder, or sub-folder, but make sure all the additional external resources used by the Login.html page are inside the images sub-folder.
I'm also working in a simple API, with XML search query responses, enabling the possibility to present data in custom pages, or on, not web, interfaces.
Regarding the Index page. Yes, you can add an Index page, and even run a complete web site (with php, perl, ISAPI or CGI interfaced applications, MySQL, etc. , support), from the PDFE HTML Server.
Just create your site additional pages at some local disk folder, and point the PDFE WebServer, Additional Options, Web Server root directory, under the General Tab, to that folder. Look at attached image.
If you put a Index.html page at that root folder, it will be the first page to be load, if guest users are enabled.
If you are a experienced web developer, you will not have big difficulties, but, if any, just post it here. Or drop me a PM if you need to send an example, not public, file.