Hopefully the PO left the floor in place so you basically have a symmetrical car to start with. I'm a relative newbie but I'll throw you my .02 and see if anyone else agrees or disagrees.
I think I would be inclined to hang the doors on the car and make sure they don't sag, are closing nice and you have a nice line between the door and the rocker. That should be a good approximate benchmak. Then hang the front fenders and line up with the door and check all gaps.
I suggest doing that first b/c the rear quarters are already off and the replacements will never be a good benchmark for reference. Once doors and fenders are on and aligned nicely you can start to massage the new quarters into place to mate the body lines properly. When I did my drivers side quarter I found that the quarter panel section that mates to the rocker right behind the door was about 3/8" too long and would not allow the quarter to drop down enough to mate the body lines. I had to straighten the flange, cut 3/8" off, re-flange it and then install. Lined up nice. Anyway that's what I would do, right or wrong I think it will get you going. Just remember that the door and fender can be tweaked a little but those quarters are fixed.
Good luck. Keep us posted.