Here's the problem. A defect in TMO leaves your stock game corrupted after you remove it. So go ahead and remove TMO, then uninstall and reinstall SH4 to ensure all your stock game files are correct and original files. Now if you are thinking ahead you'll make a separate write-protected directory to contain all these original game files and call it something like \SH4Pristine. Then whenever you have game corruption you can restore original files from there.
When you're changing from one supermod to another, it's very important that you don't try to play TMO gamesaves in GFO, for instance. There be dragons there. So use MultiSH4 to make a GFO savegame/settings directory in your \Documents folder.
Now you can play with different mods all you want!
