How do these plastic guides (entry/exit points of the hidden cable routing) come off? Do you just pry them out with a screwdriver or is there a trick?

Have you decided on a strategy to fix the ovality of the top tube? I would probably not even touch it, 2 mm of ovality in a steel tube is nothing. My Giant Terrago has steel tubes that are ovalized on purpose. In any case, it's unlikely to have a measurable effect on strength (if anything - more 'lateral stiffness and vertical compliance').