You probably didnt do anything wrong. None of the old Mopars where built "exactly" the same as far as measurements are concerned and you would be hard pressed to find to vehicles where the tolerances were identical, there are deviations on all the cars in all different locations. The headers are designed with just the body style(i.e. A,B,E etc) not the individual car and as no 2 are exactly alike some guys need to tweek here and bend there just a little to get things to fit, especially headers, even TTI's. I know it sucks but if you have to take a mallet and put a ding in the headers to get some clearance or bend a brake line or whatever, sometimes that what has to be done it doesnt take much and its the easiest way in most cases. Wow i'm out of breathe!
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