This is on another board I'm on, 4 stroke but should be about the same, for troublesome CDIs, if your getting ready to replace it anyways you have nothing to lose:
"I got an old trx300 Honda in the shop yesterday with no spark. So I did the usual check, the plug, wire, ohmed out the coil, checked the power switches. I found nothing wrong. While digging on line for a wiring schematic, I ran across this trick that bakes the
CDI (Capacitor Discharge Ignition) box in an oven for ten minutes to maybe regain its function. So I figured what the heck. 10 minutes at 280 degrees got her piping hot. Sure as heck the dang thing fired right up. Apparently this trick works the majority of the time on any CDI (Capacitor Discharge Ignition) box from pretty much any type of machine. I guess it boils moisture that creeps in over the years and shorts out the chips set. Who knew? Too bad I don't own much of the old school electronics. "
Although your wife may get upset about you cooking parts in her oven