I have got it all working now.
I did find a few bugs when getting everything working how I wanted. In FileUploadModule.cs, about Line 107 in OnProcessPostFile the following line:
Context.Response.Write(string.Format("{'success':false,'error':\"{0}\"}", Coolite.Utilities.StringUtils.Enquote(e.Message)));
should read (note the double escaping on {{ and }}):
Context.Response.Write(string.Format("{{'success':false,'error':\"{0}\"}}", Coolite.Utilities.StringUtils.Enquote(e.Message)));
The next problem I am trying to fix is that this data is put into the stream but then a ThreadAbortException occurs on Context.Response.End() which causes the Exception HTML to be put into the response (attempted to modify headers) which then measns the JSON object is broken on the client.