Tools you'll need:
10 mm wrench
12 mm wrench
19 mm socket with large ratchet
Not really a tool, but you'll also need the correct size shims. I got the 16 shim set from Fred at Arrowhead:

Make sure the engine is at TDC: the "T" mark should line up with the groove in the threads. All the cam lobes should point away from each other.

Loosen the raised 12 mm bolts on the cam chain tensioner. Remove the chain tensioner by unscrewing the two 10 mm bolts. You may need to encourage the removal a little bit...

Stuff the Abyss of Doom with clean rags (if you drop something down the Abyss of Doom, bad things will happen; your dog will die, your wife will leave you, your kids won't do their homework, and all your beer will be warm. See what I mean? Bad things!) Remove the cam cap bolts making several passes (try to keep somewhat equal force on each bolt as you undo them. Only a little bit at a time.) Put the parts in a safe place. When you remove the cam caps, be aware that the dowels will try to jump out when you aren't paying attention; so... focus.

96 or later: remove the chain guide. Three bolts, 8 mm all around. The two bolts should be problematic with falling out. The single bolt will be a problem. Grab it before it's unscrewed all the way.

Use some wire to hold the chain up. That can fall in the Abyss of Doom, too, ya know.

Remove the cam shafts. Start with the intake (the aft shaft) - pull the chain away from the teeth, and roll the assembly CW while moving it forward. For the exhaust shaft, pull the chain away from the teeth, but you don't necessarily need to do the rolling thing.

The shims are now exposed. If the notch around the shim is not readily accessible, use a small flat head screwdriver and spin it around to wherever works best for you. Pop the shims free (the oil is holding it down). You'll probably need to hold the shim bucket down while you lift the shim.

Record the shim size in the proper place on the shim sheet.

Shim size calculation video will be up soon. (Not sure exactly when. Sit tight.)

Before you put the new shims in, clean them off. I used a moist magical rag (seriously, it IS magical!) and wiped them off. Put them in their spots number side down (so the cams don't rub the size away).

Reinstall the exhaust cam shaft first. Make sure the engine is at TDC. Taughtify (that would be "pull taught") the forward section of the cam chain and set the cam in the cradles. There will be some lateral wiggle room. Make sure the arrow and tail on the outside of the gear points forward and is level with the top of the engine edge. Do the same thing with the intake shaft, but the top chain section needs to be taught.

96 and later: install the chain guide. The two long bolts are a piece of cake, the short one is normal, but the circumstances make it sneaky. Mine had some red loctite on it when I removed it, so I re-red'd it before I put it back. Don't drop it!

Put the cam caps back on, left set first (with the oil tube). Don't forget to put any dowels back in place. Lower it evenly. Screw in the cap bolts finger tight for now. Put the right side caps back on, one at a time, evenly, finger tighten the four bolts for now.

Now seat the shafts. Do the left side first. Front to back, the bolts are 1 2 3 4. Tighten them as 1 3 2 4 (front exhaust, front intake, back exhaust, back intake). Do the same sequence on the right side. Tighten a little bit at a time, working your way up to 106 in * lbs.

Reset the cam chain tensioner. A new gasket's a good idea. Install the tensioner (the two 10 mm bolts). Put the 12mm bolt with the spring and washer / gasket back in. Make sure the two 10 mm bolts are tight before doing the 12 mm bolt!

Spin the engine CCW a few turns to push the shims all the way in. At TDC with lobes pointing out, check the clearances again. Make changes until you're satisfied.

Replace the plugs.

Finishing the job is in the Valve Check video:
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Learn how to adjust the KLR 650 vlaves in your motorcycle in order to repair or maintain your motorcycles valves using tips from this free video. 
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