Hi Alex aligning doors can be very tricky. The car is probably been in an accident and suffered some damage, sometime in its history. So anyways what I do is first put some blue masking tape or some tape with weak glue on the fender side and the door side, so that I do not chip the paint, and so I can get the tape off without pulling the paint off. You can take some of tack off the tape by applying it to a cloth a couple of times it is just acting as a buffer. Then gently lift the door up and down a little to see the condition of the hinges. If they are somewhat tight, I will then look at the reveal or the gap in the door from top to bottom and around the door to see what is wrong. Most the time the hinges have sagged and it sounds to me like your top hinge is weak. If the hinges are kinda good and you still have a gap at the top and little gap at the bottom, there are some carpenter tricks that I have learned. If you take and put a couple of small washers in behind the hinge between the post at the hinge, what will happen is the door will now lift up and line up depending on the thickness of the shim or in this case washes. You can lift them a little, maybe a ¼ or more depending on the length of door and this helps the operating of the door somewhat because it puts some of stress back on the other hinge.
My experience with tr3 is that the roadster body design lacks support at the posts. Roadsters because they are open cockpit give up some structural strength especially the ones with removable windshields. The fatigued sheet metal will actual tear right up the cowling from the toque and rolling of the body on normal driving. I am not sure on a tr4. What you might have to do is pull the kick panel and actually stiffen the hinge side of the body tub. I would hold off until you are ready to paint because this usually requires welding. The fabrication is easy (just angle iron) if you are crafty common sense will lead you through it.
George