-- Yep, all pre-2.3 patches are incorporated;
-- you can see all css changes here
(note that stylesheets have been abstracted in 2.3), and I'd suggest that aside from the normal backup that you'll be doing anyway (:D) it's probably not a bad idea to save your stylesheets, and even install a demo OJS 2.3 to test them out on;
-- Are you talking about uploading a custom header in Setup Step 5, or do you mean that you've made changes to tpl files? I wouldn't worry too much about the former as that information should still be saved/moved over, but if you've made code changes, of course you'll have to track those.