Well, I'm not a vetrinary, nor have I made any actual research, but just from looking at a few pictures of horse skeletons I have discovered several things that the wrong size. I noticed that while most of you bones are the right shape, there are either not enough of them, or the ones you have are the wrong size. Sorry to bring out tiny details, kinda like Davdud101 said, I don't want to sound critical, just give suggestions for improvement.
Here is what I find would make it more proportional:
(1) Fix the ribs first, I know you said they were difficult to make, but the ribs are what give the biggest indicator of size for the rest of the entire body. Right now there are too few ribs, They should go all the way back to the middle of the 3rd vertebra up from the pelivis(count three vertebra to the right side of the pelivs, or add two more ribs, one on each vertebra).
(2) Next enlarge the shoulderblade until it forms with the hump in the spine, that will make the arms look more powerful.
(3) It appears that the head it actually supposed to fit the ribs. Take the head and turn it 90 degrees so it faces up, then move it over to the ribs and use the rib directly under the most prominent vertebra to measure the length of the skull. Scale the skull until it fits that rib vertically, then it should be the right size... I think....
Don't use the "non-uniform" scaling tool, I think you have the right shape already.
Hopefully that helps. I know it's alot to fix, but stick with it.