One very important part is to get the hinge pin as close as you can to the skin of the panel it is mounted behind. Using the stock hinges would be perfect actually, I used 55 Ford F-100 hinges when I did it to a VW bug and they worked great.
It is a pretty complicated project, making the hinges so they are perfectly aligned with one an other is one key. You can do this by bolting a piece of rectangular tubing to the hinge part that will be bolting to the door. With the two hinges mounted to the tube like this you can make your mounts in the cab all the while the hinges are sort of "one" and will remain so until they are bolted to the cab and then remove the tube and make the mounts on the door.
With the stock hinges you would simply mount them exactly as they are on the front so your door will have the hinges mounted to the inside like the front leaving room for the window channel.
Personally I think the time is better spent on other details that you see all the time instead of something that is only seen for a few seconds when you get in and out.