The bike won't run with the choke off??
There has to be something else wrong. Did you check the where the pilot screw was set? How about checking to see if there is enough idle speed screwed into the carb.
I can believe the bike being jetted too lean, but not so much so that it won't run without the choke on.
I've been slowly testing in different jetting on my 2004 FE550E, but even stock it ran okay, other than popping a little when you'd chop the throttle.
I had done a little research on my bike before I even went to buy it. And since I run on "closed courses" I asked the dealer to put in the alternate jetting listed in the owners manual. If you're not sure, look at the jetting for the FC's since they are not EPA legal, IE closed course models.
And, I'm not so sure that having "blue" pipes is a direct reflection of a too lean condition. The other night I was getting ready to load up my bike for a weekend of sport, for some reason I had it running in the driveway, not long mind you, and in the darkness I could see that the pipes were glowing. All modern fourstrokes will light up the head pipes when left sitting still. Anyway, I've seen allot of head pipes on allot of different vehicles, and all the ones that were chromed were blue at one point not far from the head.
If I'm wrong here please let me know so I don't go one looking stupid.