I would check your vacuum lines and the IAT sensor - make sure its plugged in. if the bike doesnt read proper vacuum, it will run super rich and if it doesnt read any critical sensor, the FI light will come on.
What all is done to the bike? If you have a power commander did your battery die while it was sitting, if so the PC could have forgotten the code and it will kick the FI light on if your mods require the PC to run.
I recently got the opportunity to play with my IAP sensor and all of the vacuum lines - if it doesn't not read enough vacuum, it will dump a ton of extra fuel. It should read vacuum from all 4 TB's. I eliminated all of the extra emissions stuff from the bike and made the mistake of not getting it right the first time. it runs but not very well, lots of popping and backfires... terrible fuel mileage..