Two things I see you are missing.
First, there is a primary drive reduction which reduces the crankshaft rpm before it reaches the tranny. I don't have my CR250 shop manual handy, but it is probably approx. 3:1.
Secondly, you are measuring crank and wheel rpm in revs per minute, but you are trying to measure speed in miles per HOUR.
If you stick with your current model and divide the speed you got by the primary drive ratio, then multiplied by 60, you should have an approx speed at 10,000 rpm in first gear given the wheel size, gear ration and sprockets you gave.
FWIW, I would guess your CR250 makes peak power at more like 9000 rpm, and most have 13 teeth front sprockets.