I'd suspect the window end before the head unit end. There are two different windshields. Come to think of it, wasn't there some kind of adapter for windshield V2? Has your windshield been replaced? Maybe they never connected it back up.
I was told by a person at McIntosh (around 2005) that there was an antenna amplifier next to the antenna. Now that was when they were at Ford testing their prototype audio system and I don't know if the production cars had that. I will look at my notes from back then.