Do you have a manual and a multimeter to ohm the coil with? Do you know anyone with a 97-01 so you can swap cdi's to rule that out.? Have you gone over the harness to make sure there are no breaks or shorts in it? Just a few thing that I can think of off the top of my head this early in the morning.
1999 Warrior Lonestar +2 a arms, swinger, Durablue +2+4, Renthal bars,sprockets, ITP beadlocks, Trail Tech lights, DG skids, nerfs, bumper, PRM wide grab, Spider grips, CFM airbox, Uni, clutch cover cooler, Big Gun exhaust, Works Black Widow fronts