On the rough running: check that the throttle cables are seated properly. The battery was replaced, so there's a good chance that's what's wrong.
http://www.ukgser.com/forums/showthread.php/92541-Why-s-My-Bike-Running-Rough-A-Common-Fault
I agree with FlipFly about removing the servo. Like you, I was adamant not to remove my servo when it was working because I thought regular servicing would keep it working. It failed at 30k km. It was immaculate inside but a pressure sensor inside had failed. Luckily, it failed when I was bimbling along a country road, not riding at speed. You seem to have your mind made up, though, and I know how annoying it is when someone on a forum tries to convince you of something you don't agree with, so I won't say any more.![]()
Useful thread that, thanks for the linky. Will check out all the suggested fixes. The fast idle cable was not seated properly,same as the picture on the thread where the outer part was resting on the adjuster, which was the problem the previous owner had. Not had the bike running yet due to lack of time.
Cheers