Phill, it is possible to fit a 1000ds engine in a pre '98 SS frame. Look here:
http://www.ducati.ms/forums/showthread.php?t=55069 
I don't know what is the weight difference between the two frames though.
Many people racing SSs cut the rear part of the frame and install subframes similar to the SBK ones. They are lighter and in case of a (big) crash, you could get away by just replacing the subframe only. Are you allowed to do that on your race bike?