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I have a problem with customising the skeleton. The character i am mocap-ing has very long legs and does not fit the "rag-doll" in Arena. I tried to manually assign the markers but the whole figure became messed up.
Does anyone have a good solution to this problem?

You should be able to increase the length of individual limbs in Arena. This should help with your problem. You will either need to adjust the performance to accommodate the longer legs or adjust the resulting animation. Hope this helps some.