You might want to take a look at this, about fixing file associations, in your case LNK:
http://www.winhelponline.com/blog/file-asso-fixes-for-windows-7/
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Mods can be a pain; even if they aren't "harmful" they can cause BSODs etc. But they shouldn't do anything if they aren't active = they shouldn't affect your basic Windows OS, unless you play them.
Roughly, we seem to have many methods of help that don't help, as well as many factors that aren't supposed to affect. I would
1. Uninstall Battlefied and the mod - after saving game saves on another place, for future use. I would use Revo Uninstaller for this, including clearing of registry parts.
2. I would use CCleaner or Advanced SystemCare to get rid of extra garbage - use default settings, that's safe.
3. After reboot, had I a standard HDD, I would defrag it - SSDs don't need defrag, but it doesn't harm them.
Finally, if nothing seems to help, save your personal files on another disk or partition, and make a clean installation of Windows. In any and every case, you should have a separate disk or partition for Windows vs. your own files: it's inevitable that you must reinstall Windows one of these days, and having your System and your personal matters separate will prove to be of great advantage.
"Hope I don't wear you down".
Quite often the rocky road is the fastest one.