Can I KDP just a part of my story collection?

No, if something is in Select, it can't appear anywhere but Amazon.

I'm saying Yes to the original question: can you KDP Select just a part of your collection. But that part cannot be available anywhere else if it is enrolled in Select.
I think that is right.

I think a quick email to amazon would sort it out quickly.

If I'm interpreting it correctly, the question comes up a lot. The exclusivity clause refers to Amazon having exclusive rights to a "Digital Book." Some people have questioned whether the "Digital Book" as it's put in the terms of service is the "book as an object" or "the book as the contents of the book." In this case the "object" being a single short story published as a separate publication as compared to a different "object" consisting of an anthology of stories among which is the story. Ie, can you bundle the story to get around the exclusivity requirement.

Amazon has always interpreted the exclusivity as meaning exclusivity of content, which I'm guessing is why the "or a book that is substantially similar" is in there. I've heard of people who've gotten angry letters because there were excerpts on their webpage that got picked up by the Amazon search engine.

Katie and Spell are right. When you opt in to KDP Select, you cannot have the content of that book available anywhere else, including in a collection. Once the 90 days are up and the title is no longer in Select, you'd be able to have that content available anywhere you like. Hate that exclusivity clause.