I decided to just go ahead and replay it from the beginning. It's a real trip to play the early levels with complete mastery of the controls. I felt totally invincible. Weirdly, I'm actually encountering bugs this time through. I don't know why my first time was mostly glitch free, but this time I've had a couple of freezes. The first time I got hit, the game froze for half a minute. After getting the Katana Giri, it hard locked the console with a black screen when it tried to load the next scene.
Oh, and thanks for telling me to use long sword movements. It detects the actual direction of my slashes a hundred times better, and it's really not too different from the way I was playing it before. I guess my concept of "short movements" doesn't match Ubisoft's very well, and that must have been my problem.
Even if my scores can improve, though, if the game forces me to replay using automatic weapons, it's going to be impossible to improve accuracy by much. Not to mention what a bummer it is to not get to use my favorite pistol(s) whenever I want.