is it sparking at all?? It could be either your coil, stator or pickup. I don't think these bikes have a CDI to them, but if it does, it could be that. You can check your coil easily with a multimeter, and even your stator...as long as you have the right numbers to know what your looking for. You could start by checking for a short between your coil and ground, and your stator and ground if you don't know what the resistance is suppose to be. I will look in my 99 cr 125 manual and see if it tells me...otherwise call honda and ask them what you should get for resistance readings.
Hope that helps.
~FOX~