Re: Water leaks in from front passenger door (sorry, long!).
First, obvious thing to check is if door is sagging and if so why. If you're unlucky, the top hinge has begun to pull out of the unibody, and will require welding. This should be done before you try anything else, because it will just get worse with age.
If it's just sagging from hinge wear or overall misalignment, you can get some relief just by raising the latch pin in the frame, so that the door latches higher. thi pin is just a bolt - turn it and it loosens, and you can shift it around a good deal then retighten. There is a limited range in which raising the pin will raise the door without causing a collision. Try it this way first. If it's sagged too much the latch will bang against the pin unless you bodily lift the door. So you must also raise the door, either by fixing the hinge pins or removing the shim from the top hinge and putting it into the lower one. Keep an eye on the gap between the door and the front fender, so there isn't interference there.
If the door sag is taken care of and the top still doesn't seal, you have a couple of options, depending on how finicky you are about body lines. Ideally, when latched, the door panel should be quite flush with the fender and the leading edge of the rear door (or the quarter panel on a 2-door). You can adjust this by moving the door on the hinges in front, and changing the depth of the latch pin in the rear. When this is done, if you still have a gap on the top, you have a choice. You can either bend the top of the door, or sacrifice the fit of the panel by moving the whole door in further. The better solution is to pull in the top a little. This is actually easier than it sounds. Roll the window down, and sit in the seat with the door slightly ajar, and your knees braced against the body of the door. Now reach up to the top of the frame and tug, not too hard, a couple of times. Check fit and repeat until it is where it belongs. Old doors will flex outward with long use, and this will help fix the problem. Alternatively you can use a piece of 2x4 or similar non-marring object as a lever to tweak the top into shape. Be careful not to overdo, and try for even fit fore-and-aft as well.
My 87 had roll pins in the hinges, and these are standard 1/4 inch pins, available at tractor stores and the like. You will probably have to get them a little longer than the originals, but that's all right, because if you put them in with a little extra length at the top, when they wear again, you can just pound them down and get some more wear out of them.
