Last Hurrah,
Nope, all of those you describe (3 areas) are normal. Our is like that as well.
The seal around the tails is not needed - when you removed the tailight, the 'seals' are actually where the bulbs plug in.
The rubber strip accross the top of the headlight is there to fill and stop rubbing with the hood.
The rear door seal ends 6" from the bottom of the door but if you open the door you will see the seal across the bottom of the door is what keeps water out.
All is well...dont fret
In our short off-road excursion, we didn't get any water inside.
Chris