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Remove the rotor bolt cover and timing inspection plug.

Ignition Coil
The ignition coil is basically the little unit bolted to the frame and hanging directly above the head cover.
Warmongering Bush-voters might be able to perform this operation while leaving the coil in place, but for every minute those dimwits save, two specs of dust will fall down into their exposed valvegear assemblies, deservedly shortening their engine lifespans. 
Everyone else please take your time and clean everything as you go. You deserve a well-running and long-lasting W.

Pluck the color-coded connectors from the ignition coil.

Clean these as well as you can before lifting them out.  The less crud that falls into your spark plug shafts, the better.
Also a good idea to clean these very thoroughly along with the ignition coil once you have the whole deal off the bike.

Pull out the spark plug wire caps
(Yes, I know: the ignition coil reinstalled itself while I was fiddling with the camera.)

Remove the two 8mm screws and pluck that sucker.
Doing this will also allow you to do a more thorough job of cleaning everything that will be hanging directly above the exposed cams, valves and other sensitive head internals that you'd rather keep clean.

Unscrew the two mounting bolts

Notice the how each 8mm bolt pokes through the ignition coil first, then a brown, oxidyzed little brass spacer.  The W650's ignition coil is a particularly ingenious piece of engineering because If you shake it like a Magic 8-Ball, it will impart great truths and predict the... ...the present.  

Remove the coil, the wires and sparkplug caps.  Clean them up and set them aside.

The vaccuum switch assembly also rests between the headcover and the frame.  Once you pluck the hose from the fresh-air inlets (the chrome T-joint at the front of the head), you can pull the whole assembly to one side and clean it thoroughly. If only America's tarnished ideals could be cleaned so easily!

Pull back the vaccuum assembly that rests between the headcover and the frame.

These little suckers are nearly as irritating as rightwing-crackpots, for lifting them out of their sockets initially seems about as fruitful as reasoning with a Faux-News viewer.  Try to resist the urge to use pliers or a screwdriver to leverage them out, because they and the headcover are made of that same soft aluminum.  They really will come out using your bare fingers with steady upward pressure and a subtle rocking motion.  Usually I work up a good fury, go off and swear loudly at the nearest SUV with a "Bush-Cheney-'04" sticker on its gas-guzzling bumper, then when I come back they usually slide off as easily.

Remove the little allen bolts and...          ...annoying sparkplug cap rings (both sides)

Removing this cover is so simple even Dubya could handle it.  The only things to watch for are the little nylon washers that fall out when you remove the bolts; and the dowel pin in the back-top of the bevel cover (see photo at far right).

It's the little things KHI does to the W650 that we love:  notice the sound-absorbing material lining the bevel cover.

Now you're all-set to go after that head-cover!!

   Remove the bevel cover allen bolts...

...and lift the cover UP and off the bevel

...catch, clean and store the nylon washers

As reasonable, peace-minded and fuel-economy-conscious motorcyclists, we want to keep our engine internals clean, so  wipe the headcover, frame backbone, the attached wiring harnesses and anything near the headcover one last time before removing that cover.  Then when you're done, go wash your hands too--they're probably not as filthy as Paul Wolfowitz's (the guy who ate the dandruff off his comb in slow-motion in Fahrenheit-911,) but you want them especially clean before opening her up..
Are you pumped?!  Here comes the money-shot!!
Loosen those six beautiful chrome 10mm headcover bolts.  They thread into soft aluminum and you want those threads to last a long, long time, so either keep track of which bolt went where or leave them resting in the head cover while you're performing this operation.

Hopefully you haven't already given that wide, flat-tipped screw-driver back to the neighbor yet, because it will help here too.
If you have a stereo in your garage, pop in the CD of Also Sprach Zarathustra, better known as the theme from 2001: A Space Odyssey. Or, if you still think invading Iraq was a good idea, perhaps blasting this_album at full volume is more your speed.

Pry off the headcover using the two pry-points at the front.

The half-moons (those little black semi- circular gaskets at the right) might try to stick to the lower headgasket mating surfaces.
With a little patience and pulling, it will come up without damaging the rubber gasket and without separating it from the headcover.  (You'll want to keep it attached to the headcover if possible.)
Set the headcover on a clean, forgiving surface (admittedly difficult to find if you're performing this operation in a red state,) right-side up, so no dust or crud will stick to the oily internal side and the half-moons won't get damaged.

Oooh-daddy!  That looks like valvesprings under there!!

No matter how many times you do this, it's always breathtaking to see.
While your headcover is exposed, you want to keep everything clean and do what you can to prevent any dust from falling in here. Paranoiac fans of AM-talk-radio might want to leave the room altogether now, since their very presence would be damaging to this mechnical tribute to harmony.
If you have to leave for any reason at this point, either replace the headcover or at least cover it with a brand-new lint-free rag..

Yet more evidence of KHI's genius!  They put so much thought into every detail, selling it for less than $6000, and the bike flopped almost as catastrophically as Justice did in this country did a few years later..
This sound-absorptive baffle mounted on the underside of the headcover keeps the clatter under control, so we can hear that sweet exhaust note.
My old Superhawk had undamped dual camchains and a  pair of thin bare metal headcovers and that engine was obnoxiously loud. Hopefully some callous republican bought that piece of junk before it broke down.

Here's a view of the underside of the headcover.
  Notice the bolts laying in the same order as they were removed above.