martijnP

Start by freezing the rotation of the bones.  It's easier to control them that way.

1: You can then use xpresso to link rotation of the joints.

2: With a bird like this and this relatively simple joint setup. It's not that hard to animate it by key frames.  Then you will also be able to offset the animation for a more fluid movement.

3: For a cyclical animation like this,  it's also possible to use Cmotion for parametric, looping animation.  It's a bit harder to set up if you've never worked with that, but re-timing and changing offsets is a bit easier than with key frames

I've added a project with these options

 
bird flying_v2.zip

I don't have Arnold for C4D, so i can't check this myself.
Colors like that can be make with Mograph field colors.
This tutorial shows how Arnold can render field colors:
 

Here is a simple setup,  I hope that helps.
- I made a cyllinder,  added 3 joints, bind them together.  Added 2 keyframes to make it easy to check if its working.
- Add muscle object.  Set 2 anchors to 2 joints. Then placed the 2 endpoints of the muscle object so that the muscle is inside the geometry, and at a logical place.
Fiddled around with relaxed compresswed and extended settings ( I disables autovolume and used the set button in extended and compressed states at different times in the animation)
- Added MSkin after Skin object. 
muscle_test.c4d

Maybe this helps:
 
I've made a point object (empty polygon object to which I added points manually). The deformer makes it into a sphere.
Cloner object to put spheres on each point. If you want precise control over all the shapes and sizes, you can make as many child objects as you have points and edit them individually
a Xpresso setup to move null objects to the position of the points that you can use for exporting 3d data.
Chart-10_v2.c4d