The flange pipe on my 2006 9400 with an ISX was just like Bad Monkey mentioned. 4" at the turbo and expanded out to 5" at the other end of the flange pipe.
you are right. the exhaust is 5 inch. Is it better to have one 5inch stack vs dual stack? if the similar truck has dual 5inch stacks vs single stack, what would be the diff - mpg wise?
Going back to your reducer question, just get rid of the restriction, since you already are in need of changing the the pipe,. That's what I would do. Less restriction = more power