Repair Permissions messed up network preferences
Since several files appear to be either missing or corrupt, now might be a good time to check that you have a good backup of your data and then see about booting to a Recovery HD or other bootable media and seeing if the disk catalog itself needs repair.

You might also have a technician look at the hard drive if there are lots of problems with the disk. Most can be fixed by wiping the drive and then reinstalling the OS and finally restoring your applications and files from a backup. Of course, corrupt files like you are seeing in the network preferences could get backed up in a poor state - so you might still need to find and clean things one by one, but hopefully this is the extent of the problems.