If you receive an error of the form certficate cannot be found in the local computer store during the claims-based authentication or the internet-facing deployment wizard then check that there are no duplicates in the certificate store.
Open certificates for local computer and check that there are no duplicates on “Issued To”. This is likely to be a problem when renewing a certificate where you have the old and the new one present. Ensure that there are no duplicates and try the CBA and IFD wizards again.