I'd suggest you start watching your local craigslist ads for a complete motorcycle that's been in a wreck and had front end damage. You might actually find one of these at a lower price than just the engine, and you'll be sure of getting all the correct accessories you need like wiring harness ignition coils, air cleaners, throttle/clutch cables, exhaust, etcetera.
When you buy just the engine you don't really have any way of firing it up to test it out and just have to take the sellers word that it still ran fine and didn't smoke or have any other issues when removed. You also gotta figure that if the bike was wrecked, it was probably running alright at that time. You'll also get a title that'll kinda help prove its not just some stolen motor the cops are still looking for....
You might also end up with some other spare parts off the motorcycle you could use on your kart. Some guys end up installing motorcycle disk brake setups, lights horns and switches. After your done striping it of everything you want you might be able to resell the rest.