Double check the screw settings are the same for both. All the way in, then back out 2.5 each. Then I'd say ballance the carbs! I remember someone saying the couldn't believe how often they do that... And it's a good idea to do it every time you fiddle with something. A liiiiitle difference in blue between the pipes is ok. Also, after adjusting it will be hard to tell what is new blue and what is leftover... Unless you polish the bajezus out of them.
