Sorry for dredging up an old post, but thought I'd give an update in case it's of use to anyone with similar problems in the future. After taking the car to a body shop and not liking their estimate, I waited for a while until I had some time to deal with it myself. The door hitting on the bottom was definitely due to the door sagging, and had been doing it for so long that some of the paint scraped off the part of the car where it was hitting, and was even rusting some.
(sorry for the google photos links, they don't seem to work inline)
Scraped and rusting metal under the door:
Showing how far off the door alignment was when closing:
And a final one of the lower hinge. Probably difficult to see in the photo, but it looked like the bushing was gone on the front part. The pin and hinge appeared to be rubbing and wearing, causing some rust to form as well.
Ordered new hinges and paint for the repair. Replaced the top hinge as well, even though it looked OK just to be on the safe side.
When replacing the hinges, there's a few things I discovered. The service manual list MANY things to take apart so the hinges can be addressed with the door on the vehicle, up to removing the fender and separating some foam from it. I opted to actually remove the door from the vehicle to make it easier - plus I was expecting to need to do some work on the bottom of the door as well. Although I had a good surprise with that, in that the plastic part on the bottom of the door appeared to cause all the scraping and there was no damage to any paint on the door itself. Having quickjacks made this easier, as they make a nice platform, with a piece of wood, to support the door for removal/installation.
There is an electrical connection that needs to come off for the door to be removed. I hadn't dealt with this specific type before, but it wasn't difficult to figure out. It has what can only be described as a "handle lock", which points down in the installed/locked position. Rotating this up and against the wiring itself will pull the connector most of the way out. Pulling the connector the rest of the way with the handle fully unlocked will release it, and will also lock the handle in the unlocked position. Installing it automatically releases the handle, and then rotating the handle down will pull the connector firmly into place.
As for the hinges themselves, the top one only has a rotational adjustment. The bolt that is nearest to the door goes into a pin that sticks out and gives a specific position for the top hinge. The other bolt goes in normally, which provides some adjustment room to rotate the hinge. It needs to be rotated so that both hinges are "in line" and the door will contact both simultaneously. I found it useful to use a long level against the hinges to ensure they were both at the correct angle.
The bottom hinge is the one that provides the real adjustment. As I was installing them with the door off, and didn't have any tools that could loosen the bolts with the door on, I had to do a few trial and error attempts. Basically, install hinges, install door, determine if too high/low, remove door, adjust hinges, and repeat. Sounds tedious but probably still easier than the approach in the service manual.
Now with the new hinges the door closes perfect, and the parts cost me a fraction of what a body shop wanted for the same work.