I'm glad you have progress, but I'm wondering why mirrorbone didn't... mirror bones for you.
If I run TSMBuilder and install the default bones, then select the "body" bone and run MirrorBone with its defaults, everything mirrors as we would hope.
However I find that if I select a bone on the arm or leg, i get incomplete mirroring. If I select the "1 right hand" bone I get a result that looks like what TNT got.
Just to try, you might select the body bone before you invoke MirrorBone if you hadn't done that previously.
MirrorBone ought to be a one step replacement for TSMFlipper.