
There can be several reasons why you would see uneven plug colors, some reasons are worse (more expensive/more work) than others.
Poor compression, worn parts, weak ignition/spark, etc, can cause it.
You can still get uneven plug reads even if there's nothing "serious" wrong.
Most common reason is a poor vacuum synch. If the carbs aren't synched well, different levels of vacuum will draw different amounts of mixture. I always tell others here that the carb synch is a basic part of jetting and you can't get accurate reads or trust the reads if the carbs aren't synched well.
Many owners adjust the various mixture screws/pilot fuel screws/air screws incorrectly too.
Float levels may be a little different.
Worn jetting parts or damaged o-rings will factor in here.
I personally would never set jet needles at different positions or install different jets across to repair a problem. That's what I call compensation jetting and it doesn't really work. Other problems will come up sooner or later. I suppose if you have no choice (money or enough knowledge) and it's a matter of the bike simply running or not, then it's your bike. I've seen it all when it comes to temp fixes to make up for the real problem.
Adjusting the various mixture screws at slightly different points is nothing unusual though. These screws are meant to be the pilot circuit's fine tuning that's needed because there can be small differences in each cylinder. The screws can come straight from the factory set a little different from each other. I doubt they are set beyond 1/2 turn difference though and usually are closer, within 1/4 turn of each other or better.
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