Already posted this but theres a piss-easy first fix.
Unscrew the plastic trim plate that sits on the floor to hold the carpet down and remove it. Then gently pull off the first 3-4 inches of the thick moulding that goes over the metal edge of the door opening (should be colour-matched to the carpet).
Then empty a tube of silicone sealant either side of the metal lip that the moulding covers, and all the way across the area the plastic trim sits on (thick as you like, the more the merrier, but certainly enough to fill any gaps).
Then push the edging trim pieces back on either side and refit the plastic trim plate to squish the wet silicone to form a perfect seal - if you put enough on it should be oozing out all over the place - if it doesn't, then you didn't, but you can always wait for it to go off, remove the trim plate and add more. For good measure I then put a very thin bead all round the outer edge of the trim and edge cover (paying special attention to the area at either end of the plastic trim plate where the water usually enters), wiping it flat with a wet finger.
Hasn't leaked since.
If you want a photo with arrows I can do that but hopefully its self evident.
The water tends to run down the outside of the door opening and underneath the plastic trim plate. Its worse if your truck is nose heavy or paked on a slope facing downwards. Bugger all to do with the door seal, at least in my case.:thumb2
