The problems are fundamental in this piece, tweaking it wont solve them. The pose needs to be more carefully considered, I mean the shape of the entire thing as one object. How does a real monkey stand or sit? Right now you're just constructing individual piece and trying to hook them together, but you can't do that you need to think of the entire thing at once, and then work out the details. I can see right now that the details are your main focus, like getting the samurai stuff right, but none of that matters if the basic form is off. Just draw with like one or two greys until you knock out a form that looks like what you want. If you do it this way then the silhouette will need to be clear for it to make any sense.
Also, I agree with SilentRoomate about the angles. Even while running, there should be twisting and bending that prevent this perfect alignment.