Also, take a look at the injectors.
I don't have FI, but my carbs had backed themselves almost all the way out of the air intake and it was taking in way too much air and not enough fuel. Don't know if that will help, not exactly sure how the injectors are positioned.
'04 1500 Classic
National Cycle Heavy Duty Touring 21"
Cobra aftermarket pipes, rejetted
Kury ISO grips
Mustang passenger post cover
Willie and Max Saddlebags