I just replaced a motor in my pregen. By the time that I sourced a parts bike with a good engine, tore the MC half apart to do the swap, reassembled everything, and fine tuned it - I would have been better off selling it as is, and picking up another 250 to start with. If you can find a decent 250 for around a grand, you might want to consider selling yours, and going that route.
Again, just my 2 cents.
This wasn't the doner bike, but how far I had to get into mine to do the swap! A few more steps, and I would have rebuilt it from scratch!