Success!!!!!
I have finally found the trick to making back ups of safedisc 2.51 protected games.
So far I have made 100% 1:1 working copies of:
Medal of Honor - Allied Assault, Madden 2002(safedisc V2), Grand Theft Auto 3, FIFA World Cup 2002.

Thanks to all those who offered advice and put up with my whining.

just use clone cd with cloney its so easy !!!!!!!!!!!!!1

Yeah, that's what I did. I used Clonyxxl to find the settings, then ran Clonecd.