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All 2nd gen lightnings (99-04) have superchargers.
I believe only the 02 & 03 harley supercrews had superchargers, the earlier supercabs had no engine upgrades and were N/A.
I learned a cool trick from a buddy that owns a 2000 HD Screw. He said if they have the solid orange straight line running down the side they're nicknamed "flat-liner's" due to their lack of the s/c. Not sure if this is the case 100% of the time and you could always come across a sleeper.