Hi,
If you cannot have the sender remove those extra elements under the Head node before the file goes to BizTalk for processing, I would suggest you build a custom pipeline component in the Disassemble stage (of the receive pipeline) to strip those elements off before the message is debatched.
See the following blog for more information on how to go about building such a component:
blogs.msdn.com/…/how-to-develop-biztalk-custom-pipeline-components-part1.aspx
Good luck.