where is the water ingress? normally the wind noise is from the window not seating right... John-H IIRC has a how-to on adjusting window, I dont think there's much you can do about the door itself, but I'd check all the sealing strips round the frame and maybe give them a wipe-over with some silicone lube...
Only adjust the door if the body line is out. This is rare. The wind noise is more than likely due to the window mounting coming loose.
Firstly most broblems with this are caused by the glass becoming loose, often because people push the glass to close the door and the mounting bolts work loose. Usually it's the back two screws and not the front two. You can waggle the glass and compare with the other door to see if it's loose. There are Torx screw bolts accessible with the inner dooor pannel off and the window moved down a little (the sub frame doesn't need to come out as shown here ).
The next possibility that needs checking is the alignment of the door itself - does it sit flush with the body and are all the lines true. Sometimes the striker plate latch bar needs moving, but this is rare and more than likely due to sombody fiddling with it before, due to the same issues as you're having. Don't adjust this if the door sits true there's no point.
Presuming the above is OK, then the glass angle is adjusted by slacking off the locking nuts (two off - at rear and front of door underside) in between the four front/aft locking bolts arrowed - so leave the bolts (arrowed) locked and slacken the two big nuts in between:
This allows the sub frame to pivot on the front and rear fore/aft position adjusters (don't slacken these):
Now, to adjust the glass angle. You need to move the sliding bracket inwards and outwards by turning the long screws. Adjust "Rear angle adjustment" and the equivalent "front angle adjustment" - evenly with the Allen key:
Adjust the window angle so it presses into the rubber the same as the good door.
It's possible to twist the frame slightly by adjusting differently front and rear but ideally you don't want a twist as it will increase friction in the runners. So adjust evenly front and rear. Turn allen key anti-clockwise to angle window inwards.
Then tighten the locking nuts on the door underside and replace all covers etc.