It's amazing what a bit of sleep can do...
Here is how to load swfupload via an ajax (ish) call.
Scenario:
I call some html via AJAX and write it to my document. This HTML contains the elements for swfupload. Once the elemtns are written to the document, I then create the settings var and call a new SWPUpload instance (swfu = new SWFUpload(settings)). You need to ensure that all the js libraries are included within the parent page which the ajax is being called from. Easy!