There was a comparo of those two bikes a few months back, I think it was in Motorcycle Consumer News. The Yamaha trumped the Honda in every single category, it seemed to be in a completely different class. The only thing that they preferred on the Honda was the throttle response was a little smoother.
Is the intention to ever use them on the street? If not, then why not get a dirt bike for the trails and a track-only bike for the track? Either would be a better choice than compromising in both environments. For the price of that new Yamaha, 2 used bikes would be a piece of cake to find. If the intention is to ride it on the street at any point, a Ninja 250 > either of these SM singles. Better power, handling, range, comfort, you name it.