I have not made a WR250R into a WR250X, but I have owned both bikes.
1) On my WR250X, I used a 49-tooth rear sprocket.
I felt that gearing ratio was ideal for the power output and characteristics of the engine and transmission.
Gear spacing from gear-to-gear felt very good, and I easily cruised at 50-60 mph and had a top speed of 80 mph.
I felt that was pretty impressive for a 250cc single-cylindered bike.
1a) I went with a 49-tooth sprocket for the obvious reason:
The stock rear sprocket has a WR250X ridiculously over geared (too tall), and I believe this was in order to pass some sort of drive-by sound test conducted during the pre-production phase of the bike by the Yamaha factory, not because the stock sprocket was the best choice for performance.
2) If converting a WR250R to a WR250X, I would MOST DEFINITELY change to a motard-spec front rotor AND caliper.
I felt the stock brake setup of the WR250X was very good.
I also felt the stock brake setup of the WR250R while on the street was on the average-to-weak side.
I believe the easiest way to do this is to buy or trade your WR250R parts for WR250X parts - front wheel, wheel spacers, front wheel axle, brake rotor, caliper, brake line, master cylinder, fork guards.
Install some new HH-rated pads, and ride.