There is a quiet "whisper" out there that sugsests that the Hall headers were made in bulk, and never quite right from the start. If this "whisper" is true that would account for part of your problem. From the collector to the tailpipe/muffler the best vendor supplied system may have to be tweaked to get proper fit and the correct mufler angle/spacing. Your problem will be that the car must be on a "drive on" lift for this to be done, and you will have to find a person with skill to do the bending of vendor supplied of scratch made pipes. I personally know of a vendor supplied, complete stainless steel system that had to be tweaked considerably to fit. IMHO this is the largest deficiency in parts supply.
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