I've done 3 valve checks and 1 shim replacement, never had a problem working with the throttle body in place. I did ruin the grommet where a hose attaches to the airbox, so have mostly stopped leaving things hang by hoses/wires while doing work (except oil reserve). It should be noted that the timing sprockets on some 650GSs have marks that are 1/2 tooth off. On mine and in another video i watched it was the front one being a little high. If you use a TDC bolt for a check it would best be to verify this initial position of the cams...