Well, I finally figured out my FoCal issues w/the 5d3. It's snowing here in the Baltimore area and that gave me a bit of down time to spend playing with it. Hopefully this will help others out if they are having a similar problem.
It seems that FoCal will not perform the phase detect autofocus step if the AF-ON button is not configured to "Metering and AF start". I had mine set to AE lock (hold).
I've e-mailed their support, and hopefully this will be added to the configuration changes the program makes before it runs it's tests.