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The 01-02's are preferred because they already come with the LS6 intake, no EGR, and better flowing exhaust manifolds. But the 98-99's had a slightly bigger cam and injectors. 98's have less tunable computers, and less desirable center bolt heads. There are other minor differences, but those are the bigger ones.
None of these differences should be of a huge concern. I wouldn't turn down a good deal on any year, but like a said, the 01-02's are just a little bit better, stock. Depending on your planned mods, many of those differences are mute.
My SS is a 98 and I couldn't be happier with it. I wouldn't trade it for any comparably modded 4th gen SS, regardless of year.
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