Unless you know Microsoft's checksumming algorithm for there list of critical system files, you'll have to disable WFP and keep it disabled for the duration of your modified kernel32.dll. Service packs can update it easily by moving files into the cache, setting the checksum and then asking for a version update.
To actually update it yourself, your probably best off using dos, which, if your file system is ntfs, you'll need NTFS4DOS.
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