1. Why do people say "rear" cassette?
2. 25t to 28t doesn't necessarily mean you need a longer chain - don't change it unless it doesn't pass the big-big test.
3. 28t is not too much for Dura Ace, and it doesn't have anything to do with the cage length.
4. B-screw will almost certainly fix your issue.
5. The top pulley is the "jockey", and the bottom pulley is the "idler" or "tension" pulley.