The chances of something being wrong about the doors themselves is unlikley. Once youve eliminated that you are left with correcting what the real issue is or doing what you can to get the gap and look you want. If it is the framework around the door being off due to frame distortion or a previous repair that was not properly fitted, you might want to correct that. That may be a tough row to hoe and it depends on how deep you want/ need to go. 1/4 " is a lot to be off but if you can save the swage line, one quick and dirty option is to cut the edges of the door to where you want them and use some welding rod to remake a rounded edge to achieve the gaps you want. The doors would never be useful on another car but that probably wouldn't be your worry. Just imagine some other owner saying " what in the world did this guy do here"?
These cars are a never ending story. I've heard of folks filling the door gaps with lead and then using a thin cutting wheel and some filing to obtain " perfect " gaps all around. If this all sounds like cheating, my philosophy is that there are few rules for doing sheet metal as long as the foundation is solid. If a soggy frame is really the problem it needs to be addressed but if it has just been tweaked you have more options.
For increasing the door gaps at the rear pillar, if small increases are all that is needed, it is possible to shave material off the hinge face where it mates to the door or front pillar. I doubt you could get anything near 1/4 inch this way but I had to use this option on one door and was happy with the result. The hinges are quite moveable up or down and in and out as long as you aren't ruining the swage line match you have some leeway there. Due to the swage contour the doors can only be in one spot to match. Doors can be a bugger.