[ERA Chas]

kRAMER,
You actually have two problems going here.
"...could not get them lined up in the back."
Been here done this. If you mean the tip won't line-up in a verticle way, the pipes must be removed, the collector area heated and pressure applied to move the sidepipe tip up or down as you need. This is easier to do if you cut and flange the collector to make the sidepipe a bolt on. If you mean they won't align closer or further to the body in a horizontal plane, the fix is to remove the individual head pipes and shorten them a carefully measured amount to bring the entire pipe closer to the body at the tip. This worked wonders on mine and gave the pipes a neat, tucked look to the body. It's all best judgement and trial and error. Work slowly, little at a time. It's worth it. Add material to the head pipes to space them further from the body. None of this is fun or easy and you'll have to refinish the pipes when done. See my gallery for finished look. Sorry I don't have in progress pics, I was cursing too much.

"I used ALOT of persuasion to get them to mount up in the back."
DON'T RUN LIKE THIS. If they're under tension they will snap something at 100MPH and you've got a problem. Ask how I know. Get everything to align and slip-fit bolts in their holes without tension.

"...I noticed the passenger side pipe seems to have migrated such that pipes coming out of the space in the body are all the way at the top of the hole if not touching the body".
This is the second part of your problem. The engine torque will RAISE the driver side pipes in the hole and LOWER the pass side-taking them away from the body in your case. If the pipes now sit close to the top but not touch, the worst is you will bubble the paint a little. Remember if you shorten the head pipes as above you will move the sidepipe UP in the body hole. The correction here is what the guys said: unbolt the mounts, loosen the transmount and shift the motor slightly with a hoist. Keep checking the location by lowering the motor to sit flush. YOU DO NOT WANT ANYTHING HERE UNDER TENSION WHEN ALL SNUG. Watch your radiator hoses and throttle linkage while this is going on. Fuel line is OK. "Cheat" a little to find the sweet spot with the body holes. Do all this before you attempt to get the rear sidepipe attachment right.Hope this helps.
PS-Forget the motor mounts and chains. Your mounts are brand new not delaminated. You're not drag racing are you? The limiting bolt through the mount is the best fix for movement but your problem is alignment.