You have the right idea, make them distinctive. Quote them, capitalize them, use italics or bold or underlining.
However, if you really want clarity, make them words that are not spelled the same as any other words in the document, or make them a combination of words that cannot occur anywhere else in the document.
Like instead of calling it "pen", call it p-e-n. Or if some group names itself "10 miles", always write "the group 10 miles".
I wrote a mathematical paper in which I referred to something as a Representative vector. But never just as "the representative", or "the representative vector", for clarity it was always the two words "Representative vector" or "Representative vectors" with "Representative" capitalized.
If you want your writing to be instantly clear, don't invent ambiguities when you don't have to. Clarify with more words when necessary (e.g. I can't change the name of a group like "10 miles"), or invent words that don't conflict with existing words, or make them stand out in some way that is unambiguous.