First of all you really should have adjusted the doors before the rubber. Then you install the rubber and shut the door on the first catch and leave it that way for a few days then try to shut it all the way. But the rubber needs to be smashed a little at a time.
But to bring in the door in at the top you will probably need to bring it out at the bottom.
Don't try to make it perfect until that rubber is a little more happy there.
If you look inside the hinges you will see a hole at the very back. For some reason they didn't use the bolts at the back of the hinges on these trucks like other GM vehicles. At least I don't think they did, I have never worked on a virgin truck so maybe people just left them out over the years? Anyway, if you look way at the back of the hinge you will see a hole in the hinge and in the metal behind it.
This is a '55 Sedan at work, you can see the bolt back there.
So you can put a bolt and a nut in there and you will have a LOT more adjustment on that front edge of the door going in and out. If you move that front part of the hinge in it's going to bring that door in a LOT more than if you just move the hinge in. Moving that front of the hinge in or out moves the PIN in and out and it moves the door a lot!
Brian