Watched this because I didn't think it could be as bad as everyone said it was. But it is, sorry Shakespeare. The bonus level is lame the first time, not to mention the 10th time. It doesn't seem like you are using any special powers, so just forget about it.
http://home.comcast.net/~f_amoroso/Shinobi-TheAxeMan.fcm
Here, I've demo'd the first level for you, over 40 seconds faster. My boss fight is terrible, but it's still faster than yours. A high-quality run of the game might be ok to watch, and it would probably be at least 3 minutes shorter than what you have now. With a little planning, experimentation, and a few times through you should be able to pull it off. Good luck!
I have to say this is pretty lame for a ninja game. I know you're not supposed to mess with a ninja, but this is one pathetic ninja!