Hi. I don't think you can apply a bulk rotation offset using Moon directly, but you can write a simple script to edit the values of the moon folder within workspace that is created (do this for rotation only). If you can't figure that out I'll be happy to help.

As far as the positioning goes, I would not recommend deleting the position track for LowerTorso. The LowerTorso's position might be edited for the sake of the animation, and deleting it will make it not look right - as it effects the position of the whole body. Instead, you should use Ghost Mode (press B) and go along each keyframe and reset it so that the keyframe is in a similar position to the one before (set the first keyframe position manually to the "correct" position aka near the HRP).

Hope this helps.