My theory is that a big source of confusion has been: Is stamping supposed to solve all linking use cases?

As far as the design, the answer is no. There are lots of different linking use cases and stamping is meant to solve the ones where the user wants to just manage 1 item instead of 2. Where they want to put into practice the GTD notion of "Put the thing where it means something to you."

An apt analogy I think is, until fairly recently, there has only been 1 affordance for users to add semantics to information: Folders. ie. This email is about design, it goes into my Design folder. Now that we have tagging and labeling, users have a choice about which affordance they use to add semantics to items.

If I want to COLLECT together a list of the things I need to pack for a trip, I can create a collection called packing list and throw packing list items into it. If I just want to attach a LABEL, I should be able to just type it in right on the item.

So it's the same with Stamping. If I want to just quickly stick a wedding invitation I receive in the mail on my wall calendar, I can do that with a Put on the calendar stamp. However, if I want to create a reference to a bunch of Contacts as an Invitee of an Event, I can do that with a separate affordance (ie. DnDing^? Contacts into the Invite field, typing Contact names into the Invite field, etc). But those are 2 different use cases with 2 very different affordances.

And just like we've done for Labeling and Collecting, we should provide easy ways to allow users to flow from one use case to the other:

For Labeling and Collecting: you can drag a Label from the detail view to the Sidebar to treat it as a Collection)...

With Stamping we want it to be easy for users to go from Stamping (creating 1-to-1 relationship) to generating 1-to-many links (ie. You put a Spec on the Calendar and the meeting about the Spec generates a bunch of Next Actions, thereby creating a Task thread, aka Clusters.) We've done a bunch of design explorations in this area, but Clusters have always been a later feature, though I think I've managed to have it moved to within the 1.0 sticky plan. The storyboard exercise will definitely cover this. How 1-1 relationships can grow into 1-many.