Most of the mods are coming in the patch.dat/fat files, so everything you need is:
1. Backup your own patch.dat and patch.fat files from the far cry 3/data_win32 folder
2. Copy new patch.dat and patch.fat files to the far cry 3/data_win32 folder
To uninstal you should just restore your own patch.dat and patch.fat files to the far cry 3/data_win32 folder