Just be aware that '06 is probably completely different than '03/04. My understanding is the '05/06 are similar but they made some significant changes compared to the previous years. Don't remember exactly what though.
Frankly, if it was me, I would do an '06 setup on it regardless of what year the motor is. Pretty sure the sensors can be swapped if need be so the motor won't care. I think the electronics of the '03/04 make it a bunch more work.