I don't have extensive experience updating from MSXML to System.XML, but so far I've found the two to be remarkably similar. That might be luck, if the footprint of MSXML my code was using just happened to be relatively small.
As far as it goes, Mobilize.NET published a guide mapping some common classes (not sure if it is 100% comprehensive) between the two, which I have found to be accurate:
+-------------------------------------+-------------------------------------+
| Class | Maps To |
+-------------------------------------+-------------------------------------+
| MSXML2.DOMDocument | System.Xml.XmlDocument |
| MSXML2.DOMNodeType | System.Xml.XmlNodeType |
| MSXML2.IXMLDOMAttribute | System.Xml.XmlAttribute |
| MSXML2.IXMLDOMCDATASection | System.Xml.XmlCDataSection |
| MSXML2.IXMLDOMDocument | System.Xml.XmlDocument |
| MSXML2.IXMLDOMElement | System.Xml.XmlElement |
| MSXML2.IXMLDOMNamedNodeMap | System.Xml.XmlNamedNodeMap |
| MSXML2.IXMLDOMNode | System.Xml.XmlNode |
| MSXML2.IXMLDOMNodeList | System.Xml.XmlNodeList |
| MSXML2.IXMLDOMParseError | System.Exception |
| MSXML2.IXMLDOMText | System.Xml.XmlCharacterData |
| MSXML2.tagDOMNodeType | System.Xml.XmlNodeType |
| MSXML2.IXMLDOMCharacterData | System.Xml.XmlCharacterData |
| MSXML2.IXMLDOMDocumentFragment | System.Xml.XmlDocumentFragment |
| MSXML2.IXMLDOMComment | System.Xml.XmlComment |
| MSXML2.IXMLDOMEntity | System.Xml.XmlEntity |
| MSXML2.IXMLDOMEntityReference | System.Xml.XmlEntityReference |
| MSXML2.IXMLDOMImplementation | System.Xml.XmlImplementation |
| MSXML2.IXMLDOMNotation | System.Xml.XmlNotation |
| MSXML2.IXMLDOMProcessingInstruction | System.Xml.XmlProcessingInstruction |
| MSXML2.IXMLDOMDocumentType | System.Xml.XmlDocumentType |
| MSXML2.FreeThreadedDOMDocument | System.Xml.XmlDocument |
| MSXML2.FreeThreadedDOMDocument40 | System.Xml.XmlDocument |
| MSXML2.DOMDocument40 | System.Xml.XmlDocument |
+-------------------------------------+-------------------------------------+
If you're very lucky you can just substitute old for new and run it.