Um, stupid question time: Since it sounds like you are already using XML (or could), and already have an XSD (or two), why aren't you either:

• Changing the input and output programs to use the SAME .XSD. Then either end can validate the document against the XSD and assume that if it is valid it will work. Or,
• Using an XSLT to get from one format to the other. If you have XSD for both, then you should only have to build the XSL transform once, and just run it on the data as it goes through.

It just really sounds like you're making this too hard. Or I completely don't get it.

Footnote: For those wondering what XSLT is, it is an XML application that defines transformations that can be applied to XML documents. It can convert XML to XML, HTML, or just about anything else.