There's some sort of answer below, but first... why? The CGI scripts will need a shared secret to communicate securely, how is this going to be arranged? I think you might want to look at setting up an ssh tunnel between the two machines if you are sincere about securely passing information amongst scripts.

Now, for your question, in a fashion. You could look at using MIME to encode your binary data (UPDATE: since with large chunks you should be POSTing). Another alternative would be to use Crypt::CBC (which supports Blowfish), and the encrypt|decrypt _hex methods.

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perl -pew "s/\b;([mnst])/'$1/g"