Everything is going to flex once the suspension is in and the car is on it's wheels. You may want to wait until the car is on the ground before you start aligning panels, especially if its going to take some drastic measures to align those panels.

 

The rear of your car is might be sagging with the way you have it sitting. I have hung a 1/4 on a lift and had great gaps. When I put it back on it's wheels the c-pillar closed up at the top on me. On a unibody car the 1/4 is part of the frame. Loose fit the springs and rear and set it on stands under the axle housing. This may change your gaps. Also fit your deck lid and tail panel before you weld anything. Once everything looks good and you have drilled your plug weld holes line EVERYTHING back up again and screw it together( use alot of screws you can easily plug weld the holes later). Keep checking the gaps as you go the panels can move on you from the heat. Good luck

 

The bottom pic tells me everything I need to know. The reason the panel is to close at the bottom is because the car has sagged due to the back end hanging over . I can also see that you have no support at all maintaining the body alignment. I suggest you get a bottle jack, or floor jack and place some type of pad on the jack and raise the back end of the car a little bit at a time . You'll see how the gap at the bottom opens up to the proper proportion. You always need to brace up the unibody before you start removing metal. Same goes for torque boxes and almost any panel. You can get away without bracing if you are just doing some minor metal removal, but anytime you are this deep into structural integrity you need to take steps to maintain the original frame/panel alignment. It's far from a lost cause, and by all means don't start cutting up the new skin. Just take your time and tweek the alignment until the panel fits. I suggest you also not weld the panel into place until you have the taillight panel fitted and aligned. They all weave into one sweet looking ride so you need to keep that in mind. But make sure you remember to have fun. You'll get it. You'll see.

 

great post there. Im waiting on a pssanger door to come in so I need to learn as much as i can before i go to work on my quarter panel.

 

I had the same thing happen to both qaurter panels. I managed to get it too fit by using relief cuts in the skin, where it wraps aroundthe door jamb. I only made the cuts where neccesary, and only cut through the skin. That made it possible to work the leading edge of the panel to match the door without bowing. I then mig welded up the reliefs and ground smooth. You would neverknowhow crappy it looked. Take your time.

 

Mustang Montly had an article (26739) on this type of repair. You might want to review it for tips.