The 03 2 stroke will fall short of the 05 4 stroke. If you were talking an 05 and an 05 ,, then it would be much closer,,,,but the 03 doesn't have the design built into it to handle the low end torque that an 05 4 stroke will give you.
If they are both set up so they can come off the line full throttle with no hesitation and shifted properly I think you will be surprised to see how close they really are. I was on the two stroke and did drags with the four strokes and the only difference at the end of the drag was who got off the line the best. After both came off the line,,,, and we are talking pure power,, you really could not pick one to always beat the other.