I know I promised this post a long time ago but thankfully I have been very busy.
The reason I started looking at the HTML part was to insert JQuery and my own script into the page. Being asynchronously loaded into an Iframe meant no real help when it came to modifying elements on my page. So I started searching elsewhere. I then stumbled on the Site Options on the Site ribbon in SPD.
To Add JQuery:
- Open SPD -> Site ribbon -> Click Site Options
- I chose to edit wh_footertext
These values are really there for adding consistent information throughout the site but work very well for including anything as it does not appear to be validated in any way.