Is there a way to scale a bone along specified axiis only, eg I want to shorten along y and widen along z and X?
Select the whole bone in edit mode and try Alt+S. for Y-only scaling, you may just have to move the head or tail, unless “S” confines bone scaling to Y-only. I’m not sure, I’m new at this. 
The simplest way is to grab only the desired axis in the Scale manipulator (red=x, green=y, blue=z), using the Normal coordinates option for the manipulator, which orients the manipulator to the bone’s local axes. You can use the Shift and Ctrl key as modifiers while doing this (Shift = fine control, Ctrl = stepped values, Ctrl + Shift = finer stepped values).
Or, enter values in the Transform Properties panel’s Scale fields.
You can also use keyboarded numeric entries – select the bone (in Pose Mode, of course) and use S-KEY (for Scale), <axis label – X-KEY, Y-KEY or Z-KEY> ,scale value on the NUMPAD (e.g., 1.15 typed on the number pad of the keyboard), ENTER. This can be very fast once you get the hang of it, as well as highly accurate. This example would scale a bone by 2.0 on the Z axis: S-KEY, Z, 2, ENTER.
Be sure to keyframe the new values!