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What choke do you have? The EFI system has no "choke", but rather a hand throttle adjustment that barely moves the plates when pulled all the way out. Designed for when the vacuum solenoids are not quite enough to keep it running. You did plug/remove and seal the vacuum hoses to the old fast idle solenoids you removed, right? I took mine off about 5 years ago, and I crack the throttle just a wee bit when cold starting.
That would explain why it had no effect 
But I still wonder why it started right away on the first try but not on the second (or third) try?
I still think it was the colder air on the second try.
Maybe an issue with the air temp sensor?
I have the fuel controller and will install it to see if it makes a difference.
It's been over a year since I've had mine apart - so memory is failing me here - but doesn't the "choke" (fuel enricher) work in connection with all the stuff you took off?? Like I said, I'm not remembering the details, but seems to me they're related. I could be wrong - am quite a bit... 
My Christmas gift to me from me was an air box kit from Chucksters Customs. ( I always know just what I really wanted). I made a video of the installation with a little product review included. Over all I am happy with their product. At the end of the video after the mod I opened the garage door (it was warm in there at first) and the bike fired right up first time! Then when I tried to restart it would catch and cough but wouldn't run?
It was about zero degrees Celsius today. Could it be the cold weather that is causing the bike not to restart? I know I read reviews of guys doing the mod and having a heck of a time starting on colder mornings. I was using the choke.
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