I added a feature to folksonomy tonight that lets you explicitly define relationships between stories using Folksonomy. To do this, just add a comma separated list of / for the entries you want to be related to. For instance, I'm forcing this entry to be related to my Folksonomy Update post, by adding the following to its metadata section:

#related item/folksonomy_update.txt

You'll notice that it is the first entry in my related stories section -- explicit relations are evaluated before any others are inferred, and therefore take precedence.

This feature is available in Folksonomy 1.4