The only surefire way of sorting your problem is as follows:
Uninstall the installation via the option with the game disc
Delete the SH3 folder in C\MyPrograms
Perform a registry clean using a decent programme such as RegVac, below is a link that includes a free trial version:
http://www.regvac.com/regvac.htm
Go to the GWX website (available by clicking on my sig) and following the comprehensive installation instructions.
After the new installation is ready ONLY ADD THIRD PARTY MODS THAT ARE JSGME COMPATABLE and only add them one at a time and load the game to ensure there are no conflicts before adding a second etc.
The alternative is IMHO a lot more time consuming and tedious.
Good luck in whatever path you choose