I started to make a speedrun of this. Got to stage 6 i think and then dicided to start again with all I'd learned. However, it desynched and I backed up BEFORE i watched it(stupid, stupid).
I'm going to try again. But the main point of this post was to tell you all something I don't think you have discovered.
One of the main issues it seems, is working out if is quicker to jump, double jump, or jump with a flying kick afterwards. Well, there's one more technique:
When you throw a shuriken in midair, one of 3 things happen depending on how far away from the ground you are: If you're high enough, after the throwing shuriken animation finishes, you'll revert to regular falling status and when you land you crouch for a couple of frames, and will be stood still. If the shuriken animation doesn't finish in the air, it continues on the ground for however many frames are left of it and you will be stood still.
The trick I discovered is that if you time it so the animation finishes on teh frame you land, then nothing happens and you continue running with no input, just holidng forward. This is demonstrated on later levels, here:
http://www.freewebs.com/bof3genes/BSshinobi3.gmv because I only discovered it on the watery level, and learned how to do it reliably after that.
I know in general that run isn't really that impressive, but was my 'test' run of sorts.
Also, another thing is, when you jump(running), there is a certain distance you can fall and keep running, and will always have to be less than you jumped. So, if you have to jump over something(an enemy), try and land on something higher(like a box) and you will keep on running, and you can run off the edge(if it isn't too high) and keep running. This is demonstrated everywhere, but most notably on 1-2. You probably knew this. Anyone have any otehr general tricks/observations you can share?
I think we all agree this game is in need of a near perfect speedrun.
Right, time for me to start again, again.