Ah yes, I totally forgot to jump at the beginning of 6-2C, oops. Didn't notice this until I was done. Also, I am working on a takes-damage, as fast as possible run. I've just reached act 4-2 where damage will really speed things up on the spikes.
Unfortunately, it's not easy to take hits that help in this game. Simply running into an enemy on level ground will throw you back a bit, wasting far too much time. Being hit while you have upward momentum is even worse. So the only time you can really take a hit gracefully is falling, you don't get thrown at all but just keep falling and regain control when you hit the ground. That's why so far I've only taken 3 hits which have probably bought about 20 frames of improvement total.
Interestingly, I've found quite a few other improvements which really dwarf the damage shortcuts. For example jump down cliffs instead of falling, even if I have to wait a few frames. I've also cut off about 100 frames (~min and a half) on each of the first three bosses. Used correctly, vacuum wave can make boss kills much faster, so thanks again to devindotcom for that tip. This means I hold onto vacuum wave all through acts 1 and 3. It's not available in act 2, but I beat the 2nd boss much faster anyway by taking him head-on and balls-out. So not as much variety with the specials but I pull some nice tricks with the wave. Also, my wall-climbing jumps are even faster.
So the results are that I have cut about 9 seconds off of just the first three acts. There's certainly room for much more in the rest of the game. We'll see how it goes with the spikes, I need to hit enemies and use the invincibility on the spikes as the spikes take off too much damage. The problem is the invincibility wears out pretty fast once you regain control. But anyway, it's gonna be pretty sweet so keep checking.
I'll give you a peek at what I have so far:
http://home.comcast.net/~f_amoroso/Ninja_Gaiden_3_-_TheAxeManv2.1.fcm