You can use HTML::TreeBuilder to parse the HTML, then output it in XHTML, using the as_XML method, which works most of the time. It may not help with the encoding problem though, especially if the HTML lies about its encoding. XML::Twig can do this for you BTW, so in fact you may not need to use tidy at all, just install HTML::TreeBuilder and then use parsefile_html to parse the HTML.
Also HTML::Tidy uses a fork of tidy, and may be worth a try.
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