You might run into suspension issues with a heavier more powerful engine even though it is dialed in with the 139. It might need shock work to help it hook up properly and the larger engine mass will affect the bikes handling especially if you have to modify the frame. Also the engine will need to sit at the same angle as it sat in its orig frame.
Other things to concider:
-Will the bigger and possibly taller engine fit under the gas tank?
-You will need the carb, reed cage, cage boot-will these fit
-The frame/exhaust may need to be modified to mount the exhaust
-Is the ignition compents and CDI the same, if not you will need these also.
In the end is it worth it? Cost of the engine, required parts, comprimising the frame geometry, time to do it all, down time from "research and devolopment", if your frame work fails with you on it (hospital bill) and you will have a bike that you will probably could not ever get rid of when it was time. You probably could come up with a good used later model YZ250 and have the suspension redone. I just sold a 03 YZ250, all stock except normal wear and tear compenents (chain, sprockets, top end and some plastics) for $1800. So $1800 + $500 (suspension) = $2300 - what you could sell yours for (maybe $1200-$1400 priced at NADA.com ) = $1100 to $900 to step up to a YZ250.
As you can see, I would not take on the job. Its just not worth it weather your broke or not. I would save up and and just by a newer bike. Parts are easier to get, bike set up wouldn't be a chore and less headaches.
Good luck with you decision.