I went for another night ride tonight. The lights still alternate between dim and bright. I did notice that running the turn signal at a stop, it would flash quicker as RPMs increased. I had checked the output previously when the lights weren't doing this and it was OK. I never have starting trouble and it runs fine. I'm thinking it's the regulator. :dunno:

I also noticed an intermittent tick, louder than the normal valve noise as the engine was idling after the ride. It would come and go. 4,400 miles on it now. It's definately coming from the top end(I have an automotive stethescope). I guess it's valve time too. :dunno:

While you have the valve cover off for your clearance check:

1) Check the tension on the cam chain by pushing down on the chain in the middle of the upper run between the camshafts.  It shouldn't be loose.  (Duh, Kerry!)

2) Try to push each cam shaft back and forth along its length (side to side).  If one or both of them have a little play, this might explain your "tick".  Although the sound I have heard is more like an intermittent "soft clunk".

OK ticking or more like clacking... is valves... even valves wihtin spec... clack...
The lights going dim and bright is AC seepage into the DC circuit... aka regulator is busted. Other symptoms... mostly in other makes are a headlight that pops often, tail lights that pop, a flasher relay that quits, battery that boils water out, fuses that blow... but never had a GS with that problem before... so no idea what it does. Check your alternarot, for resistance and then swap in a regulator that's known to be good... and if that takes care of your problem... send me bad regulator... need to slice them open and see what's in there.
Cool.
Srinath.

Thanks guys. I'll try a regulator. The sound could be described more as a clunk. It is definately different than the valve noise. I hope it's nothing serious. Srinath, I'll let you know when I've got the regulator swapped if you want me to send it to you.