Compare the data, not the XML! You know what differences are meaningful, not some generic XML comparison tool/function. For example are the following two snippets equivalent?

<foo>
 <bar>1</bar>
 <baz>2</baz>
</foo>

<foo>
 <baz>2</baz>
 <bar>1</bar>
</foo>
[download]

? Well, that depends. The order of the tags may matter and it may be completely irrelevant.

Parse the XMLs you need to verify, parse the Excel file (save is as CSV, that's gonna be easier to work with) and compare the data that should be the same.