250r's will run on a 350x cdi box.
They dont run right, but they will run in most cases.
A member on here fought a no revving problem on a 250R really hard, and came to find out someone had a 350x cdi on it. He swapped back to the R cdi and it ran fne.
Give it a try.
Also wire wheel the rust off you flywheel, paying special attention to the raised trigger block welded to the flywheel, and the little pick-up on the the black box above the flywheel.
Seal that stator cover and wire harness grommet with RTV when you re-assemble.
Check and make sure the flywheel and crank shaft do not wiggle around. Grab the flywheel and shake the crank bearings. If they are really loose, time for a new crank.
Here is where my long useless list of stuff nobody cares about should go...
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