Updating System Path with a script

I am currently researching different methods of upgrading the Oracle Client software from Ora8 to Ora9 on approximately 3000 desktops. I know how to automate the removal of the old client and installation of the new one, but the system path remains a difficult obstacle for me: the new Oracle path must be in the same place as the old Oracle path, but all the tools I have seen to date (such as pathman.exe) can only append the system path. Is there a way of putting the path elements in a specific place in the path via a script? I need to automate this process to get it done in a timely manner instead of having my techs visit all the desktops just to manually edit the system path. Any ideas?