Hi Ryan.
I have never done either conversion.
I'm sure either would work.
If I am right and both can be done equally, all things being the same I would do the 03.
Primarily because I keep my bikes a long time.
I have found that once a bike gets a little older you have a much harder time finding after market parts for it.
Not to mention the newer bikes usually have a little better suspension and brakes.
On a positive vote for the 94, it does come with an engine that can be sold to help offset the cost of doing the conversion.
I'd still do the 03