have you tried to swap the ignition coils around to see if the 1+4 coil will work on 2+3 and vice versa and have you checked the pick up coil for 1+4 to see if it has a pulsing live?also i have had a bandit 400 stop sparking on 2+3 and it was the cdi that had had a little burn out inside.i sent it off to electrex uk and they fixed it and sent it back and it was as happy then.but i know you have changed that so it wont be that i would check the pick up in the right hand small engine cover with suzuki on it.as m says you do get bad contact where the low tension leads fit onto the coils on the spade terminals so make sure they are bright and clean and not dull and green or grey looking.
adam bike doctor, June 2010