If you have another BizTalk server available, you could try deploying your application there to see if it works in a different environment. Have you tried deploying a subset of your assemblies?
I did try to uninstall the original version of the dlls
What exactly did you try? E.g., have you undeployed and uninstalled the BizTalk application, then checked for remains in the GAC (.NET v2/v4)? I believe that should have been thorough enough.
I recall this System.Xml.XmlException
could occur in BizTalk 2006 when trying to update an assembly while it is still referenced by an existing port.
Deleting the port or at least the dependency (i.e. chosing pass-thru adapter) should make the deploy work correctly; afterwards, do not forget to reconfigure the modified port…
If multiple references are in place, then perhaps it might be easier or quicker to just export the bindings, delete all ports, update your assemblies and finally import your bindings again.