Custom keyboard shortcuts not working

I've been trying to set up a couple custom keyboard shortcuts, most notably Command-Control-, for System Preferences and Command-| for Merge Cells in Numbers. I had set these up previously and they both worked fine, but now they refuse to work. The only thing I can thing of that might be connected is the reason I had to set them up again, which is that I deleted all my preferences trying to troubleshoot Facetime, and while I restored most of them, some I intentionally did not and others wouldn't overwrite their replacements so I chose to ignore them.

I think at this point, I just need to wipe out the preference file that contains those settings, but I'm not sure which one it would be. There doesn't seem to be a com.apple.Keyboard.plist file, which is what I was assuming I should look for, so can anyone point me in the right direction?

jW