It's "normal" (well, "NSR normal"!) for the two cylinders to run differently at idle, but if the idle is VERY different cylinder-to-cylinder, then I would look at the compression.
If the compression is low it can cause a misfire, then as the rev's rise, things generally tend to get a bit better!
Running the motor with the RC Valves fixed in one position won't hurt the motor; just possibly make it harder to start/run at low rpm.
Andy.
NSR-WORLD.COM