I would do a visual of the motor mounts. Then check the torque and on the rear swing arm. If you have a warranty take it in. I'm not familar with fairings but I would check over everywhere you bolted the fairing back up to make sure nothing is wrong there. Also look your tires over real good for any bulges or knots.
i couldnt swear to it, but even when idling the vibration feels rougher and more noticable then it did before.
Check the exhaust bracket behind the rear head.
They have a habit of cracking.
From here it sounds as tho you have a miss in the engine. I would get it warmed up a bit first. What rpm does it idle at? Less than 1000? I would use a rubber band around the throttle grip and brake lever to get the rpm @ 1000. Now pull one of the plug wires. How far does the rpm drop? Does the engine die? Reinstall that wire and do the same thing with the other wire. Don't worry about setting codes during this, you can take care of that later. This will either eliminate the engine as the problem or it will point you to which cylinder is acting up. Keep us updated.