If the wires got bare and touched the metal while it was running, its anyones guess, but solving no spark is fairly simple in these things. You may have simply ruined the p/u coil, its located down by your stator, bolts on your case with 2 small bolts, it sends the signal to the cdi which in turn sends the voltage to the coils.
If it were me, I would use a digital voltmeter set on the 20 scale and hook into the p/u coil, and when you pull the engine over, you should see varible voltage, meaning it will show like 3.1-4.2 volts or whatever and wont be steady as you cant pull the engine over quick enuff. This means its working, then go up to the cdi box and see if you show the same signal going in???, then check wire coming out to the coils???, should be some voltage, let us know we can go from there.
the other items over there by the cdi are the smoothing condensor,voltage regualtors, the 98-99 have 2 of em.