Tools you'll need:
Torque wrench
10 mm socket with medium ratchet
14 mm wrench
Phillips screwdriver
Small flathead screwdriver
6 mm Allen head wrench (the ratchetable type is handy: you can put it on the torque wrench)

Marking the position of the controls will not be helpful if you are replacing the handlebars. I made this video when I was getting to the steering stem bearings. I didn't think my handlebars were as bent as they were...

*MAKE SURE YOU NOTE YOUR WIRE AND CABLE ROUTING!* Pictures, diagram, another bike, whatever. It's a PITA to figure it out.
















Righ side
The front master cylinder has two 10 mm bolts. You can either loosen those for now or take them all the way out and get the assmebly out of the way (make sure you support it (upright) once it's out of the way). You'll also need to unplug the two wires for the brake light switch. It probably doesn't really matter which goes where, but I labelled them anyway. I figure why take a chance when it's quick and easy enough to just label?
Life will be easier if you take the mirror off, it's 14 mm.
The stop switch assembly has one Phillips screw recessed between the red switch and the start button. Don't lose the little metal piece that in there.
The throttle grip assembly has two Phillips screws on the back / underside of the bar.
I got my (used) bike with Acerbis handguards on them, I don't know if they're stock or not (probably not) on pre-08s. It was a 6 mm Allen head to get it off the end of the bar.

Left side
The clutch perch has two Phillips screws on the front.
The switch cluster has two Phillips screws on the backside. Loosen the top, tilt the assembly forward and you can get to the lower screw.

Center
Use a small screwdriver to remove the plastic caps. The bolts underneath are 6 mm allen heads. There are 4 of them.

To put the handlebars back on, make sure the mirror mount is on the bar (the thing that I said you don't need to take off (1:51) facing the right direction - you should be able to put the screw in from the front (sitting on the bike) and have it pinch the bar, put the throttle assembly on and mount the center bolts ("finger tight" - enough to hold it in place whilst you fidgit and get everything back on). Set the switch over the mirror mount and put the screw back in (mind the metal piece that should be there...). Remount the master cylinder tight enough to hold it in place and upright. Plug the brake wires back in under the master cylider.

Put the clutch perch back on and the left switch cluster between the clutch and the grip.

From left to right, the layout should be: grip, left switch cluster with mirror, clutch, (center mounting bolts), front master cylinder, right switch cluster with mirror, throttle assembly with grip.

Sit on the bike and move steer side to side (full range of motion). Nothing should be binding - if it is, figure it out now and fix it, chances are something isn't routed right.

Find where the bar position is comfortable and torque the bar clamp bolts to 18 ft * lbs.

Rotate the switch clusters around the bar to find a comfortable button-pushing and mirror location. Butt them up agains the grips and tighten (snug) Do the same with the clutch and brake. Tighten everything down (snug + a LITTLE).



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Learn how to remove the KLR 650 Handlebar  from your motorcycle in order to repair or maintain your motorcycles brakes using tips from this free video. 
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KLR 650 Handlebar