I believe they both bolt up to the head the same. However, the lower flange(with two holes) is a different bolt pattern. With a little modification, I am using the 92-95 upper along with a 97+ lower section. It required a little welding and adding studs. The exhaust holes line up.
Aside from that, the lower section is a different shape. On 97+, the lower section dips down further, then has a sharper bend. This aimed the pipe upward towards my floorboard a bit after installation. It was a major pain in the ass, and I hit that lower section of pipe off of the pavement on hard bumps frequently. I plan on changing my header out in the next two weeks to a month.
So, it will fit, but not well, in summation.