07 was the first year for the 6 speed tranny and all Heritages had fuel injection; prior to 07 it was 5 speed and you could get fuel injection or carbed. Believe 2001 was the first year for fuel injection.
whatever you do, be sure you get a 96" with the six speed. i think that was in 07 and up, right? that sixth gear is really great, as is the increased torque of the 96" motor. to hop on one of my friends' 03 or 05, just sucks compared to my 08. cost should not be a whole lot of difference to get an 07 or 08 etc. rather than the 88" 5 speed model.