The part numbers for the stock OEM A pipe (lower part of Stock 2-piece exhaust mani) are slightly different:
99 GSR: 18210-ST7-A63
00 GSR: 18210-ST7-A64

The stock cat P/Ns are different as well, but everything else is the same. I know that doesn't quite answer the question, but I imagine if there is a difference in the cat inlet shape, that is the resulting difference in the header. But I'm not sure that will make a difference in your situation or not.