Also it is my understanding that the injectors on the 03-04 have a different spray pattern than the 04. 5 +.
Yes, that is inherent with the bowl design. The 04. 5+ is 124 degree spray angle while the 03-04 is 143 degrees. The bowl design is the main reason as the re-entrant bowl on the earlier engines redirects the pattern back to the center. The later 600 engines don't redirect but they inject quite a bit later to keep the pattern in the bowl.
Timing, angle, and duration all have an impact on smoke and power.