yea 99 tomos should have the one wire CDI/coil, it's just the black wire to the coil, timing is set by the magnets. If timing was off it'd still spark. that's not the problem. if it gets power outta the black wire it should work unless something between there and the plug is bad. I usually work back from the plug - take the boot off and see if the bare plug wire sparks held near the fins - that'd indicate a bad boot. try new plug wire, if it gets power into the box and not out well I think you've founf the problem.
Also any grounding issues or kill switch issues need to be rules out first. make sure the coil/box is bolted and grounded to the frame or motor. Disconnect the kill switch wire so you only have the black wire from the stator going directly to the box, omitting the kill switch wire. make sure that's not unintentionally grounding anywhere.
But yea, short answer, sounds like ya need a new box.