I have a 2002 Thunderbird that encountered the famous battery drain problem. My son in law (a Master Certified Technician) and I worked on it quite a few times last summer with no results. I ended up taking it to an independent shop whose owner is a top notch technician - especially Ford. After two weeks he said it was the driver door jamb switch.
It seemed okay for about three months and then the problem returned. Again my son in law and I made several unsuccessful attempts.
I then returned it to the independent shop that had it last year. They had it for over five weeks.
I got it back yesterday and they told me the problem was the battery module was "confused" because of the battery draining so many times and wasn't allowing the system to go to sleep.
They reprogrammed the battery module and watched it for several days and they are confident the problem is solved.
I have read all kinds of posts in the past trying to solve this problem so if you have a 2002 to 2005 Thunderbird or Lincoln LS with a battery drain problem see your Ford dealer and have the battery module reprogrammed - hopefully it will solve your problem.