How can i fix theese gaps? Also the door doesn't close flush with the body near the handle and lock.

 

Is it like that on both sides? With the door open, can you feel up & down slop if you lift on the latch end of the door? If so, then your hinge bushings & pins are worn. They make replacement bolt type hinge pins, but you need to grind off the original ones. And the hinges are welded to the doors to make the job even more fun.
For closing the door flush with the rear quarter, that's fixed by adjusting the striker bolt (on the latch door pillar) in more.

 

The lower pin on the door looks like its in good shape. But yes it does have some play so im guessing probably the upper hinge is shot. The other door has fairly even gaps and closes flush, but the lower hinge pin is worn right out. Are you sure that this could be fixed just by replacing the hinges? It looks like the whole door needs to come towards the front of the car almost half a centimeter, or would I just weld and redrill the holes while im replacing the hinges?

 

To adjust the doors right, you need to have hinge bushings/pins that are in good shape. The door with the worn lower pin would already be dropping closer to the fender. So if that gap is already wide, then something else is also out of whack. And you really don't want to go removing the hinges if you can help it. That's a whole other can of worms. If you only need one upper and one lower pin/bushing, and the others are in solid shape, then you would luck out by getting this:
Door Hinge Pin Kit