if only porting only the cylinder then the only thing you can do is change the exhaust port and outlet---- or get a different cylinder. 

when you port the exhaust it will need a bigger carb to match the larger flowing exhaust port and outlet.  hence the need for 38mm-40mm carb. 

- just a chainsaw file will be enough to port the cylinder like CT or any other race company.
- u just need to know the width and  height of the exhaust port to shoot for.
- it sounds like the rm250 top end might be a good way to go but im afraid the stock yz250 will still win as a guess.  he got nearly a complete factory 250 with a tuned stock carb thats big enough.