Hi, Shegeek!
I recently upgraded from 1.03 to 2.0 and then 2.1 and was able to save my old 1.03 career. So far, I have not noticed any problems or CTD's. As far as I recall, I simply made a copy of my campaign\saved folder and saved it to desktop before I uninstalled SH3 and deleted all remaining traces of SH3 from my computer. After I re-installed SH3 and GWX 2.1 I simply placed my old career into the new save folder, loaded up the game and was able to select my old career. (Make sure that your old career last save is in base and not at sea).
Good luck and let us know how everything goes!