Hey Byron,
Just a suggestion:
Try installing it from the back end towards the front. What I mean is attach your exhaust tips first....then your pipes over the axeles and into the pit bulls......keep working towards the front. I know this is what they recommend when installing the Pypes Exhaust Systems.
Perhaps it will work on the ATR system too?
I bought a used Stainless Steel 2 1/2" ATR system with Pit Bulls several years ago. I ended up taking it to a shop that specializes in exhaust / muffler work....they build custom systems too!.
Good thing I did, cause just like you, mine didn't fit very well. They had to cut and tweak one of the pipes downstream of the cat. Y connection to get the system to lay flat.....also had to cut and re-bend the drivers side exhaust from exiting muffler to exhaust tip cause it was hitting the gas tank.
They also cut off the ATR's attachment brackets near exhaust tips....as they didn't line up (reason being however they started from the front back). They ended up welding in some new muffler attachments to the back side of mufflers and also to the exhaust tips. They said that this system was heavy and needed the support to effectively support the weight.
They finally got it done, but cost a few buck$ in the process. I must say that I am very happpy with this exhaust system though. Well worth the hassles and money.
Good Luck.
dave