I've also got some door alignment tips in here:
http://www.viczcar.com/forum/topic/3202-tutorial-door-skin-removal-for-dummies/page-3
Whatever you do, don't do what I've seen and heard of other workshops doing to fix a saggy door, don't put a 2x4 of wood under the door frame and jack the car up by it's door to try and bend the door upwards. That's wrong and will destroy the hinges. If you take the non-hamfisted approach you can get the door alignment pretty good. I still have to experiment with shims on mine to see how that alters the overall fit and still need to grind down the upper skin ledge.
The thing about these cars is they have had various repairs over the years, often done poorly / in a rush and they do more harm than good long term. So you kind of have to be a detective to figure out what has gone on and why it won't align.
You can also re-pin the door hinges, there is a thread on here somewhere about it. I'll see if I can dig it up. You can check to see if the door hinges are flogged out and need re-pinning by opening the door and trying to tilt it up and down from the rear of the door, if you get a clicking and some play in the door hinge you know it's flogged out and needs to be re-pinned. If it doesn't move and is solid with no major movement then it should be ok.
*Edit found the thread here:
http://www.viczcar.com/forum/topic/10316-sagging-door-hinges/
Enjoy you can spend many hours sorting this out. Trust me. But it is worth it.