Brake servo running constantly..

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
 
Servo removed yesterday. 2.5 hours start to finish. Fitted a new rear brake pipe, its the one for the non-abs 1999 to 2004 GS, 30quid from motorworks, the angles on the unions are a better fit than trying to force the original to fit.
No wires cut-- I removed the module from the servo unit and plugged it back onto the multi pin plug.
The brake lights work with no mods to wiring or switches.

Also used the little copper brake pipe adaptor from motorworks to connect the front pipes together on the headstock.

Hope this helps anyone else thinking of tackling the job themselves.
 


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