After a lot of searching, I was able to fix the "PID file cannot be found" issue on my machine. I'm on OS X 10.9.3 and installed mysql via Homebrew.
First, I found my PID file here:
/usr/local/var/mysql/{username}.pid
Next, I located my my.cnf file here:
/usr/local/Cellar/mysql/5.6.19/my.cnf
Finally, I added this line to the bottom of my.cnf:
pid-file = /usr/local/var/mysql/{username}.pid
Hopefully this works for someone else, and saves you a headache! Don't forget to replace {username} with your machine's name (jeffs-air-2 in my case).