In response to Markus,
I checked my supply and the exhaust manifold tubes are slightly bigger on the 00-04. The 97-99 exhaust manifold doesn't have the pre-cat's, so I'm guessing they might flow better. One of the best Porsche mechanic in Texas has a liking for the early 97 manifolds because he thinks they flow better. Some early 97's have a flat spot on them and that's how you can visually tell. On that note, I took a picture of the factory manifolds that I have. Starting from the left we have a 2005 987, early 97 flat manifold, 00-04 and a 2001 996 exhaust manifold. I didn't get around to measuring, but the 996 and 987 look close to the same size.
While I was at it, I took a picture of the secondary pipes from the 986 and 996. The 97-99 and the 00-04 are the same size and the only difference appears to be the lack of an O2 bung for the 00-04. It looks like they still kept the heat shield though.
From the research I came up with, the 987 base and S share the same muffler but have different tips that attach to one 70mm singular exit tube. I would have loved to have two separate tubes coming out of each muffler at a better angle. The factory muffler has the exhaust gases exiting towards each other and then making a 90 degree turn out. I'm thinking tomorrow I'll fabricate something to help the exiting gas flow better at that point.
My modified 987 muffler looks larger in this pic, but it's only a few inches wider than the 986 muffler. It's about the same total height in the middle but a few inches narrower on the sides
