I Have just replaced my door hinge pins with the upgrade ones from TDS. I also replaced the detent roller and got a new striker. I did remove the lower hinge from the body to replace the detent roller and pin. I used the same shims on the striker. The back top of the door is not flush with the quarter. this has also caused a gap between the rear of the window and the weatherstrip. here are some pictures. Note: I still do not have the door weatherstriping on, as I am waiting for new weatherstriping. But I dont think that would cause any interference. Here are some pics

 

I would try adjusting the striker on the body a little, you may need to move it because the old hinges wore it out? Body work isnt black and white most of the time. You may have to adjust a lot of stuff to get it all to line up properly, or it has always been "off" and you didnt notice because the bushigs were worn. I think the door on my 91 GTA is like what you pictured. I know the door has been replaced but the hinges do not sag and are not worn out.

 

Looks like the front needs to come up and the striker needs to be moved towards the middle of the car..

 

looks to me like the front of the door needs to go down. And move the striker in twoards the passenger side-- not much side to side movement with the striker, I'd say move it all the was in see where that gets you.
good luck, let's us know how it turns out.
-Birdofprey83

 

Did you ever solve this? My car is doing this exact thing.

 

Top of the door needs to be bent in. Striker doesnt have to move. If you move the striker in too much it will make the door pop when you open it. Take a foot long 4x4, put it between the door and the lower part of the jamb. Then push in on the top part of the door where its sticking out. Be careful, pushing in the wrong area can dent the door. Alot of thirdgens, including my own, seem to have this problem with the door out at the top.

 

My theory on it was that previous attempts to raise to door from sagging and scraping. (i.e. using the striker pry bar tool, or just pulling up on it) This likely has bent/moved the hinges. Now that the pins/bushings have been replaced, your hinges may be bent just enough to make it not line up. It really doesn't take much for a very small bend at the hinge to make a significant change in height considering how long our doors are. I put 190lbs of me on the end of the door a few times, some what reversing has been done previously. You could use a striker pry bar tool for this as well.

Hope this helps

 

any updates?