If it is in the middle of a project from my experience what you can do is save the skin weight of the rig as preset and then place nulls on all the joint roots and end eff's of the rig to mark their origin and re run the biped guide and match translation the new guide with the the nulls in place and make the necessary corrections in the neck and spine. Now,re generate the biped rig and for the skinning we already have the preset saved,so import it.for everything else we have Gator.
I generally keep a mother file of the rig saved when I generate the rig from biped guide or from any other guide with all the origin positions marked with nulls.this bad rotation thing has given me enough pain already.
just for curiosity don't you miss a hip control in the XSI biped rig? have you modified it ever and got a hip ctrl in place if done already then good,else I made a few changes to the rig to get 1 in place its simple but effective.I am no great rigger am just an animator,but it works for me.If you wish I can share.
All the best with your production