Well, she's going to GP Motorcycles tomorrow and they're going to hook it up to their O2 analyzer to see how she's running when cold then see if they can adjust it so that it doesn't stall.
Update: Tomorrow was yesterday and the dealer said there is a motor that opens the throttle plates during cold start that is not operating correctly, kind of like an automatic choke. So, they replaced that and the sensor that controls it and are going to start it cold tomorrow to see if that cures the problem. They did state that there was an error code the bike was throwing but the check engine light wasn't on.
Can't wait to get her back running properly again... there is a big empty spot in my garage and my heart.