I have been trying to figure out what has been draining my battery. so far I have pulled the battery and the alternator both testing to be fine. I've been checking for parasitic drain but have only come across the fuse for the amplifier for the shaker 500 system to show any significant change in voltage when pulled the voltage slowly drops. When the car is running the charging rate has been 14.1. Any ideas??

 

I've had a similar issue with my car. The battery load test and an alternator check at the dealer reveals no problems.
After several discussions with a Ford tech, it was suggested that my radio, ac, navigation unit must be turned off before shut down.
This has helped but has not been a complete cure.
I pulled the Shaker 500 and replaced it with an Alpine unit and this helped a bit, but my cure has been a battery tender.
During the summer months as it sits in between track days and weekend club cruises a warm up with an idle run of about five minutes really helps too.