Cody, forgive me for asking a basic question - Comets, Fairlanes and Cougars use a 2 piece rubber isolator that wraps around the leaf springs, and so those vehicles utilize a spring pad on the rear end housing that have a large locating hole that indexes on those rubber pads. The leaf springs still have a small locating pin. If you don't have those rubber pads, and just put the rearend directly on the leaf springs it could be off center quite a bit one way or the other. Are you missing the rubber isolating pads, or are the pads falling apart? Mustangs do not use the rubber pads - they have a smaller hole in the perches that sit directly on the springs. Not everyone realizes the rubber belongs on the other vehicles. Just a thought.
I'll edit my post to say, on anything "Performance" or "Race", or if you were installing a CalTracs system, you would want to remove those rubber isolator pads, but then a person needs to make the locating holes on a Comet/Fairlane or Cougar rearend housing smaller, or make a reducer bushing, so that the housing correctly locates on the small pin on the leaf springs.