I removed all jets and verified they were clean, jet holders as well. All circuits flow air just fine. The idle circuits flow air just fine from the jet opening out the little hole. Both sides flow the same. Although much harder to check, they do flow air back to the jet opening as well. You can get a huge amount of air through those main jets even if they are actually quite small. Float needles and seats look great.
Float height was checked according to this
http://faq.ninja250.org/wiki/How_do_..._the_floats%3F They are both at exactly 17mm and no fuel in either of the floats.
This isn't my first rodeo with carbs. I've had bikes with carbs for the last 40 years. I've cleaned, adjusted, made jets, rigged, soldered, patched, just about anything you can do with a carb on a bike, I've done it.
Given that everything inside the carbs is pristine, no dust, dirt, goo, rust, discoloration even, jets are open, all passages flow, diaphrams and slides work well, floats and needles are fine, I don't believe there is anything wrong in the carbs.
It feels and acts more like dirty points or a bad condenser on a real ignition system.
If you feel it's imperative that the mixture screws be removed even though the circuits flow the same amount of air in each carb, I'll pull them and do it just to make sure.
I was thinking very seriously about the iridium plugs. I've heard so much good about them and very little bad.