Issues with reftagger

Hello. I am Superdadsuper, I am an Administrator and Bureaucrat (this means that when we are larger I have more weight to decisions, more active, and have more of a leadership role compared to other admins as well as managing them) of Biblicalapedia. Biblicalapedia is an online wiki about the Bible and its history, theology and literature. Being a wiki and one about the Bible, one of the most important things its attribution to verify everything submitted. The prime if not sole source of all our content should be the Bible and needs to be attributed to it. 

For a while I have wanted to convert the default references system on the wiki (it uses MediaWiki) and add in reftagger. Since all of our references are going to be converted to Bible verses I wanted to add reftagger as the tool to automatically link it all. I have had encountered some issues with adding it to myself, namely that the MediaWiki instructions on Reftagger do not apply as we our hosted and do not have that level of access to add it onto MediaWiki. Please note I am not very keen on JavaScript and so would like to gain some help. One thing I noticed was that it needs to be added right before the </body> tag. How would this occur (the script and then have it be added right before that tag). Also due to security issues at hoster, eventually I will not be able to use the script I got from reftagger's website. As of now I can but eventually they will deprecate usage of the script tag. I have had somebody create a script for me that would serve as the script without <script> tag. Is there a reason why that won't work (and how could I make it before the end body tag, both for the one with a script tag and the function).  I have added both on Common.js of my test site (a javascript file which applies the script to all pages but I believe the element isn't specified and isn't embedded directly on each page) and Cite References Link One file. That file allows editing of the reference system. This does not work because that loads everything before the end of the body tag. It would be preferred to do it before the end body tag but after the references. Rather than using in-line verses, all verses are contained in footnotes. Is there a way to allow it to search in the class "reference" rather than it just being in the p tags? This might be a bit complicated for the I would like to implement this very soon. Bible verse footnoting has been considered one of our site's most notable features. While we use it in a very different way (link our footnotes) we still have the same need to point to the Bible as the source.I would really appreciate it, both personally, and on the behalf of Biblicalapedia in adding this feature.By adding this feature you are helping Biblicalapedia take the next step and further centering our focus of the source of the content on the Bible itself. In Christ,  Superdadsuper, Biblicalapedia Administrator and Bureaucrat 

That does not seem to work. One of the issues might be is that I believe the "common.js" file loads before the the end of the body tag. What needs to be done is a way to take this script and have it appended at the end (I wouldn't know how to do that without replacing the current part of the script at the bottom 

 var g = d.createElement(t), s = d.getElementsByTagName(t)[0];
                g.src = "//api.reftagger.com/v2/RefTagger.js";
                s.parentNode.insertBefore(g, s);
        }(document, "script"));