Here are the links for the ninja2. The ninja walks on the floor now. The wave animation is too short, so it looks like the ninja waves and then it freezes. I added a little bit of code to enable the LOOP property and now it waves a lot more so it does look like it freezes. I'm thinking the server has a fix time allocated for this animation so when the animation is too short it just wait until it times out and then tries again.
I added in the code for the ninja, but it's a bit small. If I make it bigger, it doesn't walk on the ground any more. A scale of 0.05 seemed better, though it was hard to tell.
I just created a topic on meshmagick. To scale meshes and skeleton in the same folder. I could guess the ninja is half the size of the armored-swordsman.
I tried scale = 2 and y-scale=210 and the ninja is "walking on the ground again" You could just apply these changes. In case the ninja doesn't work for you.
I think the ninja was standard size and the armored-swordsman-look to big. Anyway. without a frame of reference it is hard to tell what is the correct size.
I just modified the ninja into ninja1, "the cyborg ninja". Actually, I just used the texture from the robot and a few minor tweaks. It looks pretty good.