First off welcome to XOC!
Second, this probably should of been posted in the Performance section.
Third, are you saying that the exhaust that you have in the box has a flange on it that needs to bolt up to the stock exhaust?
And you can't get this one to match up?
If the above is true, your 03 is like my 04 and there is no flange to bolt up to and you have the wrong exhaust. I believe there was a design change/difference between 00-02 and the 03-04 models. I know that my exhaust didn't have a flange and I had to remove the old exhaust by removing a clamp and getting the muffler slid off of the headpipe.
Check out this
Gibson On! Does the last picture that I posted look like your setup?
Hope this helps.
Rob