You could really keep it simple and use a video camera and draw key measures onto still frames which you print from the video capture. There is nothing wrong with this. You will be able to compare joint angles and deviation from CG based on lines drawn from the registration points which will presumably be marked on the horse. If I were you I would start simple. Then if you get some interesting findings you will have a good basis on which to sell your research idea to parties who may have the money to fund a more sophisticated system.
Good luck!