Guys I'm really sorry I haven't gotten back with a better drawing...I just haven't had the time. I am really glad to see that a number of folks are doing this and not paying for it. Regarding the capacitor:
1. It's there to ground out transient signals/voltage spikes. Why? they may interfere with the timing, quality and power of your spark. They may also damage upstream electronics. How? A capacitor does not allow DC such as the your 12V system voltage to flow through it, so connecting a wire from your hot 12V power in to ground through the capacitor does not ground out your system. However, a broad range of AC frequencies (referred to as "noise") will ground out through the capacitor, hence "cleaning" up the voltage. The capacitor that Ford chose for this application probably is focused on common frequencies found under the hood of the car.
2. Where does it go? The best place to see this is on your stock ignition: It runs from the 12V power wire (going to your coil) and is attached and grounded to one corner of your coil. With COP you can just re-connect the capacitor to a handy valve cover bolt at the back passenger side. If you do this right you don't even have to change it's connection from stock as it's already connected to the 12V wire ( which is why I did not include it in the original drawing). If you end up doing more drastic wire work, just make sure that you connect the capacitor's wire near where the 12V splits to the various COP plugs.
I know pics are better, but honestly if you can't figure it out with this much info you might consider getting someone to help who's comfortable doing this kind of stuff.
As an update, mine is still running strong with no misfires, codes or trouble.