Re: 04 Navigator Roof/Sunroof leak
Did you ever remove roof rack?
I also have 2004 Navigator and I removed the roof rack last year, then went for a car wash (to remove all the dirt) and it leaked in the same spot as in your case that night when it rained..
I put the roof rack back and it never happened again.
If you never removed it check the seals on it, that's where the water gets in, but when the car is moving (in my case it leaked when I was stopping or turning).