Would a yz250 or larger motor work well?
Work?...yes
Well?...yes
do you want to tackle the job of trying to Build a header pipe that requires more math then all the books in the closest college could teach you?...up to you
I'm not trying to sound like a C**K ROD, but you would need to know how the exhaust gasses flow threw the pipe and how that affects the power and throttle response of the engine. There is allot to be considered when planning an engine swap like this.
if you know how to weld getting the motor in and aligned properly is the easy part, its knowing how to build the pipe so its tuned right that's going to be the challenge.
If you have the money to spend on getting a custom pipe made by somone that does it for a living your looking at up to $600-800. for that much you could have bought an engine off E-gay and rebuilt it, got a decent pipe and some good reeds and been close without all the hassle.
Its up to you but i know what direction i would go.
There is always that little exception tho, and that's if i got the YZ250 engine for FREE! then its a case of why not, it didn't cost me anything and I'm not out much if it doesn't work.
Bet of luck to ya, hope it all comes out well in the end.