How would you fix this ?

As everyone is saying fit the door first.

Then raise the door striker pin at the quater 1/8" to make sure that is not holding the back of the door down, see if that helps the gap. Then cheat the body lines at the door to quarter just a tad high, they were not perfect from the factory anyway.

This is what you call "Steal from Peter to Pay off Paul".

So doing as much as you can with the door situation, go to the fender next.

Now if you have your car up on jack stands on the frame at the front of the transmission area, this will produce the wide gap at the at the top of the fender you are seeing.

The car needs to be down on all 4 wheels and tires on the floor so the front of your unitized body and frame is not flexing down opening the fender gap at the top.

The reverse of this is also true if you take 2 bumper jacks at the front bumper and bring the front of the car up 4" with the fender loose.

Then do your final fender alignment starting at the door gap first. Lock it down/bolt it down at the rear fender cowl and rocker panel area. Then work your way forward along the hood gap and final lock down at the core support and inner fender braces.

Then let the car sit on all 4 wheels without the bumper jacks, things should stay in place with good gaps.

It is a bit of a wrestling match flexing and moving the front fenders around until you get the gaps you need. The unitized bodies are strong once all components are in place, tightened down, and holding position.

I had quite the fight putting the front fenders back on the D100 Pickup to get the door gaps to line up. Had to flex the frame like above, push with Porto Power and pull with a Come-A-Long. Locked down the good door gap then proceeded to lock down at the core support and finally install the steel inner fenders.

Down on it's wheels and all gaps held good.

Those fenders don't just drop on, although I wish they did . . .