Harry Kim playing the clarinet was actually first set up in Caretaker. Janeway mentions to Tuvok that Harry Kim's mother had contacted her asking if she could send it along because he'd left it at home.
The rank situation never bothered me. I love Star Trek, but I never watched closely enough to pick up on those type of differences. I'd notice if someone went from Ensign to Lt, or if they were a Captain one day and not the next. Outside of that I don't know the difference. I think the majority of viewers would be the same.