It's a tough one.
I'm dealing with something very similar right now

. Bike just started missing on the left cylinder occasionally. Always when I start it after it's been sitting for several hours. After about ten minutes, it starts to fire and runs fine.
I've switched the coils, checked the gap on the pickup coil, still misses on the left cylinder only. Checked for spark, nada.
Just finished checking out the connections on the igniter. They seem clean and after plugging it back in it hits on both cylinders. Sometimes that can reestablish the connections if they're oxidized. If it does it again I'm afraid that it'll be the igniter, about $600

.
I'll do some more intensive checks this weekend.
I need to be sure before forking out that much dough.