I'm currently still searching for a way to make the animation loop properly. I have tried copying the first frame of the animation, pasting it in a appropriate frame and deleting a few keyframes before the pasted frame to ensure proper blending of the animation. Unfortunately this didn't yield any interesting results. I will continue looking for a decent way to loop the animation without too much manual editing.
In the meantime I have come across a way to retarget mocap armature data to an existing armature using the following tool. I haven't tried it yet (and don't know if I will because I'm quite satisfied with the results so far..) but it is worth keeping in mind.
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