It looks like you had more than one problem. The coil was definitely bad and needed to be replaced.
Is there a crossover pipe on the exhaust? I have one on my wife's 550.
I don't know anything about your bike but normally fuel/air screws are turned about 1 to 1 1/2 turns out from lightly closed. If you have a carb issue I would look at things that affect the mid rpm range. This would include float levels, main jet diffuser, needle settings and jet needles. I don't know what rebuild kits you used but I like Keyster....great quality. I wouldn't use anything else.
