The other thing about studying and practicing Bach is that he sounds great even at the slowest tempos. That really helps!
And you are correct that getting the right fingering down before you do a lot of practicing really helps. As far as the right fingering feeling "wrong". I don't know what to say - sometimes it feels wrong because it is the wrong fingering for you, but sometimes it feels wrong because it is a new kind of fingering and you aren't used to it (Schumann loves to do that to me).