XML : whitespace aware reading/writing of XML

I need to change some elements of an XML file and write the file with no other differences.

In detail I have a set of elements which need to have an id attribute in the xml code. I find these elements with a xpath expression and add an ID to it. But when the dom is written again, the formatting differs a bit.

1. the order of the attributes is changes to alphabetical
2. the definition of the namespace is moved to the elements (<ns1:root xmlns:ns1="abc" xmlns:ns2="xzy"><ns2:element/></ns1:root> changes to <root xmlns="abc"><element xmlns="xzy"/></root>)
3. linebreaks and indetion change

The xml is read with javax.xml.parsers.SAXParser (namespaceaware: true) and written with javax.xml.transform.TransformerFactory (indent: yes).

The best way to preserve the formatting would be to alter the source string, is there a good way to do this without diving in too deep into the xml parsing thing?

Or is there a way to parse the xml to dom whitespace aware?