Can codeigniter do this?

[eluser]tonanbarbarian[/eluser]
If you are saying that you have different DTD or XML Schemas to work on depending on the source of the xml data then simply create libraries that interact with each xml data source.
I have done something similar in an app.
It loads different libraries (hard coded at the moment) depending on the source of the xml data, but each library has similar methods so that the controller or model can interact with any of the libraries in standard ways