I imported in the same 'walk.bvh' file as empties this time, and deleted the constraints I already had. (knees, eyes, legs, but kept the master), I then had to change some of the parenting to make sure it all still matched up (toe.l - foot.l - lower leg.l and for the right side).
The empties start in the middle of blender on frame 1 but when you move on in the timeline it jumps to a different place and plays the sequence from here. Then using the 'track to' constraint I made the bones in my already made armature follow the relevant empty. It made the bones jump about into an odd shape, but when they move along the timeline one can see they are doing something.
I added in some IK solvers, to see what else would happen and it seems to move the bones slightly, they are still not attaching to the empties but really pointing, I manually moved the mesh to the empties and it seemed to become more of a body shape but as soon as the empties moved away the armature and mesh seemed to fall off it. It's not following properly...
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