Do you have the same number of topics in the new course that you had in the original? If you don't, it might work weird, but it should show as orphaned. I ran a 2.5 site for a while and then a 2.8 for much longer...I think I remember doing this successfully in both. Have you tried restoring Course 1 as a new course? OH! Wait...quiz...are your questions saved in the course question bank or the activity question bank? If they are in the activity bank, they won't ever copy (you can export them from it and import it in but that doesn't always work as expected). But if you move them to a course level bank (like the default), they will.
Questionnaire...I got nothin'...haven't used it since 1.9. Yeah, you read right, 1.9. Switched to feedback to simplify when I upgraded.