You're talking about the 125SX models in particular, I assume. The 98 and up motors are all screamers. The teething problems with the PDS that was mentioned is something I'd consider in buying a 98. They can be improved with valving but they will never be as good as the 99 and up because the internals of the newer shocks have been altered.
The 99 125SX was the only 98/99 KTM 125 or 200 that had the 50mm WP forks. Those forks are awesome and worked great on that bike so I'd lean towards that bike if you have the option. The 98 125SX has the 45 'zoke.
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John Brunsgaard - JEB
01 KTM 400 EXC, 99 KTM 250 EXC, 99 KTM 200 EXC, 98 KTM 125 EXC, 98 KTM 380 MXC (gone), 96 KDX 200