You can get away with not slotting the gears but there will be a bit of a flat spot down low . The timing Marthy quotes works the best . Pulls from 4000 rpm to redline .
Don't know why the idle changed but it won't be because of the exhaust change .
There's an idle adjuster screw on the left side of the bike . Look between the frame and panels near the throttle body for a phillips heads screw.
Not sure what your trying to do .
It will start in gear if the the clutch lever is pulled in , but not if the stand is down , there's a switch on that to .
Australia might be the only country that had the restrictor to comply with the learner approved power to weight restrictions. Go into diagnostic mode on the dash and see what your throttle reading goes up to. Restricted was 70%
You need to machine your FZ6r cam gears to fit the FZ6 cams.
https://www.600cc.org/threads/fz6-cam-install-project.32137/
It changes the power band from pulling between 6500 - 10000rpm to being 4000rpm to 11000rpm
Try testing that wire for continuity from end to end with a multimeter , there could be a break in it. Could also be a bad earth wire.
Otherwise i'm all out of ideas.