Before you re-order the ignitor box try sealing up the original. You've got nothing to lose. First, remove each ignition connection, place ignitor in a small reseable freezer baggie, punch appropriate holes into baggie, use dielectric grease on the connectors, pass the wires through the bag holes, re-connected them to the box, then zip-tie the bag around the wires. Apply silicone chaulking to the zip-tied bag holes so the bag is water-tight. Might be a good idea to also wrap the bagged ignitor box in some insulating foil to repell engine heat. Find every ignition connection, including sparkplug hookup, and apply dielectric grease. Try and seal out the moisture that is penetrating your ignition circuit. Put the bike back together, and start 'er up. Now, wet the bike down to simulate a rainstorm. Try re-starting the bike a few times under wet conditions. If this doesn't work, then try a new ignitor box. If it does work, you've saved yourself $1000.
