Here's what I would do:

1) Animate in 3ds using Cyborg biped, as usual
2) Export and compile into a separate model_animations file
3) Use Kornman's Halo Animation Editor (http://hce.halomaps.org/index.cfm?fid=577) to inject the new animations over the FRC animations of the old Cyborg; save to a new animation file
4) Set Cyborg biped to use new animation set

Nothing too scary about that.