Mark, you stated that you measured the resistance of the coils and both were the same. This is no indication that a coil isn't failing. You might have an ignition coil run poorly when hot but it registers ok when cool. Did you switch the wires on both coils to confirm the problem switches cylinders? You never stated that you did so. This is the acid test to determine if its a coil failing or the CDI going.
One last thing, do you have your throttle position sensor plugged in or disconnected? I'm curious. If it's still plugged in, unplug it to see how the bike runs? I've had a problem in the past with a bum TPS that caused all kinds of poor running problems. FWIW. Unplugging it solved the problem.
