First off, the bad news.
If this top was chopped with the doors fitting like this there is a very good possibility you are going to need to align the doors then redo the top frames to fit. I can not make this clear enough, don't be looking at how the top fits, fit the bottom of the doors and THEN look up there, you simply can't worry about the top until the bottom is done.
When after the bottom is done you want to do a little dance and make the top better by making the bottom worse or you want to bend the window frame a little or something, sure that may be done too. But not until you have fit the bottom and you KNOW the bottom fits, they you worry about the top. This actually goes for fit the top wasn't chopped too, if you want the doors to fit nice you would adjust them to fit and then "massage" the upper to fit if needed.
But if it has been chopped with those doors looking like that, you WILL need to do some work on those window frames to make it all work once the doors are aligned properly.
Ok, now that that is out of the way, is the door out at the front at the bottom too? If so, you are going to want to adjust it at the hinges and I would need a photo of the hinges to see how they are mounted, I don't remember from the very few times I have ever seen them in person.
Are the front doors aligned properly? They could be too far out at the bottom making it look like the rear doors fit at the front when in reality they don't. You need to remember fitting panels is a dance, a choreographed dance. You are pushing and pulling and moving panels all over to make them ALL work, you don't align one, then go to the next, you can do this by starting with the rear door, then moving to the front door then moving to the fenders, yes you can do this. That method is simply moving from the weld on non adjustable panels, the quarters, and making the rear doors fit them, then moving forward. However, often it takes this choreographed dance to make it all work, where you have the "bestest" fit everywhere instead of a perfect fit which without serious work may be simply impossible. It wasn't even close from the factory, these cars weren't like todays cars with perfect gaps and fit.
So, like I said, you need to look this thing over good before you start twisting doors. But this is how you could do it. This first picture is using a block of wood that stops the upper part of the door from closing and you apply pressure to the lower part of the door. Some cars twist very easy, others DO NOT twist at all, funny thing, you never know which will or won't.
You will notice my leg is pushing in on the bottom. You could get down lower and push with your hands too, but this is one way. Oh and by the way if you should try this, DO NOT wrap your fingers around the edge of the door, go ahead ask me how I know.

ain: I was doing this on a 69 Shelby GT500 years ago and the wood fell out and my finger was shut in the gap of the door with it completely latched! Oh yes my finger still shows damage from when the fingernail grew back a little different.

ain:
The other way is to pull out on the top and push in on the bottom, this is the way I would recommend as it usually works well. But again, pushing in the bottom with your leg and pulling out on the top will often twist that baby RIGHT NOW.
But look it over well before you do it, remember this is a dance.
Brian