In Utah's tutorial, you ARE supposed to rotate the body 20 degrees, as Utah felt it gives the unit a more powerful looking stance.
For the Run Animation, you should use an entirely different save. Take your unit, delete all keyframes so your unit appears in the 'crucfix'-like position, add the run animation and save as 'unitrun.pz3'.
For the other animations, the abdomen should be rotated 15-20 degrees opposite the body, so as to not mess up the direction for the attack.
Hope that helps some.