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I am curious about this PCI Compliance issue though? Are you able to talk more about this. I think others may find themselves in the same situation. And this thread might help them out.
As for IIS 6 to IIS 7, Microsoft completely revamped IIS 7 so depending on the application, you might have to do some recoding / configuration changes to make sure everything works as expected.
Consult the application's documentation to disable SSL 2.0 and use SSL 3.0 or TLS 1.0 instead.
Open to your help as to what you might suggest.