If its not the seal then you could be lucky like me and have a back window leak... I really need to pull my back glass and fix it, but some silicone has slowed it down a lot.
Might sound silly, but get some good flashlights, and fold down your back seat (if you have the folding seat) and lay down into your trunk while a friend soaks the outside of your car with a hose. It helped me pinpoint my leak.
Worst part of mine is that the car sat for a year or two with old brake rotors and calipers in the spare well and they rusted into the carpet