I was thinking of attaching a note to the bill (and tip), noting why I had "under tipped" 5%--should I have done this?
No need for the note.
In the above situation, had you left 5%, the waiter would know EXACTLY why you left what you did.
In fact, this was the actual intent of tipping. If the waitperson regularly gets low tips for poor service, they have a very big incentive to improve their competencies.