You shouldn't have to reinstall the game just because of mod installation and removal, but there is always the possibility of something becoming corrupted. One solution is MultSH4, which lets you have multiple installations of the game. I always keep a fresh untouched one just in case.
http://www.subsim.com/radioroom/down...o=file&id=1110
As for the second problem, it's not uncommon for a conflict to cause a crash to the desktop, but a complete reboot is rare. I have no idea what could have caused it, but you could try removing TMO and starting the game again. If that works, then you probably have a corrupted copy of TMO, and downloading it again should help. If that doesn't work, then you may have to reinstall SH4.
But there will be others along soon with opinions more informed than mine.
