If the headers are not designed to end in the exact factory location then it will throw everything else off. We will assume that your cats are built to factory specs. as well as your cat back starts in factory location. Then process of elimination tells us that it is your headers.
Now, my system has very little wiggle room. It is designed to fit in factory location. If the parts in front of it are not to factory specs. like I said, it will throw it off like your current situation.
This is what I was getting at about flex joints. Say you had flex joints in your current cat back, then you could fudge it and make it fit. All it is going to do is leave your exhaust in a bind and you are going to eventually blow out that flex joint.
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