Alright, so I have partially discovered my problem. msconfig exists, but it is at
So the next thing I did was add the above directory to my path, remove all instances of my "copied" msconfig, and viola! It worked. It's possible I messed up my path while editing it. Now I have to wonder what else is broken though =/
As far as OS Reinstall: Not an option. This is a production server and I can not take it down for the amount of time it would take for me to get everything up and running again.
Thanks for the help though Edge100x.