1st Welcome Aboard Herr Kaluen!!
I have had the file issue you had with the help files.
I can only suggest a complete uninstall and reinstall and patch. (Eventhough you have already done this)
Make sure you do a search for SH3 and Ubi files. Anything you can think of. Thats what I usually do and it works. I also use the add or remove programs in the control panel and not the game uninstaller.