From what I am hearing, there is really no difference in flow, therefore really no gain in horsepower. The 3's have a symmetric reed design, meaning the inner and outer reeds are the same. So no worries wether you got the correct ones when it comes time for replacement. Another thing to think about is the 2's have screws in them. Have heard horror stories of these coming loose and detroying an entire top and bottom end. Little dab of yamalube will fix that problem. The downside of the 3's are they snap together. Some guys on PS have complained of them coming apart(but w/no detrimental effects as compared to the 2's).
I personally bought the 3's. For what you pay for them, if they won't stay together, the manufacturer better be replaceing them, or coming up w/some sort of solution.