I am looking at setting up an external facing FTP server. Are there any
guides on how to secure on FTP using IIS 6? Or are there better solutions?

IMO it totally depends on the use case.
For anonymous download from the FTP only, no uploads,
then the FTP shipped with MS OS is fine.  But for upload
you should look into a secure FTP (i.e. not based on clear
text password) service.

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