Just for the sake of information, it may be usefull for someone here.
After many days of headaches and trial and error I already found the best way to use any animation for UDK, using the default UT3 Skeleton.
I have done it with Motion Builder 2013, however it may work with Maya LT (student version) aswell, because both use the Autodesk Human IK Plugin.
You need first to import the animation to either maya or motion builder. If you are using bvh mocap and you use maya you need to download a free maya phyton script which imports bvh.
The secret is so simple, the process works almost 99%, you may need to do just some minor tweaks for the animation because sometimes depending on the mesh of your character some limb may overlapp others.
The secret is that you need to go for the first keyframe of your animation and manually rotate the bones to make the character in T Pose. Then after this you need to create a skeleton definition (HumanIK Panel) which you can save as a template. You just need to tell Maya / Motion what bones are the head, arms, legs, and so on, so you will remap the bones of your animation for the HumanIK Skeleton definition.
After this you need to characterize your skeleton (create the control rig) in HumanIK Panel. By doing this you will have a snapshot of your character in T Pose, and for the other animations you don`t need to do all over again (so long as the other animations use the same skeleton structure).
So now we are done with the animation.
Next step you need to import a default UT3 Character to maya or motion builder. I just ripped the UDK Guard using unreal model viewer, imported to 3dsmax and exported to Motion Builder as FBX.
Once you have your UT3 Character in Motion Builder / Maya, you do the same procedure you have done to the anim. Manually pose the character bones in T Pose, create a skeleton definition, create the control rigs.
Now you have 2 characters ready for animation, the BVH (Mocap) Animation and the UT3 character.
The first character, the BVH Animation already has the animation, while the UT3 Character is static, no animation. You now just set the source animation of the UT3 Character to the BVH Animation (there is a drop down menu in HumanIK Panel).
Now the default UT3 Character moves as the BVH animation, almost perfectly.
Now you plot the Ut3 Character Animation to the control rig, do some tweaks, then plot the animation to the skeleton, then last you go for the HumanIK Panel and select save character animation as fbx, import in UDK animset, and voilla!!!
Works like a charm!!!
sometimes you may need to move a bit the root bone of the animation to match the standard UDK animset to avoid much offset of the animation.
Sorry for not being able to do a more complete tutorial, I just wanted to share what I learned.