Hello from Nc
Not sure what sort of special parts you'd be worried about finding for a '98, other than valve covers/coil rail hardware if you planned to swap to later model head castings. Tuning for a typical cammed/stalled setup in a '98 is not an issue for any good tuner, though a major build (especially FI) might benefit from a later model PCM swap. "Horror stories" are mostly internet hype in this regard.
My '98 has actually been my best and favorite LS1 car, as compared to my '99, '00 and '02 cars.
I prefer a stalled A4 to an M6 myself. Hard to find nice A4 cars in my region though, most are high miles and worn out. Low mile M6 cars are much easier to find as more of them were weekend toys (vs. daily driven autos). Sounds like you have the opposite problem in your area. If you like your '98 I would just keep it; there is no magic to the '01/'02 cars (and that's coming from personal experience with both), nor would it be worth selling one to get the other unless you're significantly upgrading in condition or you want an entirely different model (such as Firebird vs. Camaro).
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