Too tight on the head bearings can cause what might be mistaken for 'head shake'. What 's actually happening is the natural slight 'wobble' the bars do while rolling over the pavement gets restricted. Since it's gotta do it to stay upright, and moving bikes like to stay upright, the rear tries to do it instead. On rain grooves, it's an EVIL feeling.
"Easiest" way to adjust the bearing is to pull everything off the bars - clutch, brakes, wiring, everything! Tighten the bearing until the bars start to bind a little and back off until it will just flop to the side. OK, not so easy
My way is to get it close - that is you can't feel a clunk when you 'drop' the front end while it's on the center stand. (Press down on the rear, then let it go for the front to hit) Go right over some speed bumps, the end of the driveway, etc and feel for a 'clunk'. If you feel one, tighten another 1/8 turn. Repeat. The downside is it takes more times, but it doesn't take long each time. Plus is it's 'just right' at the end.
Make sure the fork tube clamps and front wheel are properly torqued too. I've felt them be a little loose and make a clunk feeling too.
Dan Bergman does it another way, but I've forgotten it (CRS). It's probably in the history here or over on the COG forums.
Don't forget about tire pressures, preload, etc. Over inflated tires will feel 'sharper' or 'firmer' and can contribute. Try reducing the pressure 1 PSI and see how it feels. I have an about 2PSI 'sweet spot', and I can feel the difference between the top and bottom of the range (38-40PSI - your gauge may vary).
I finally got the last remnant of on throttle shake out of mine by removing a little front preload and adding a little to the rear. By geometry it should make it worse, but I think it added a little weight up front and helped stabilize it.
Some have said torquing or replacing bad or properly shimming the engine mounts and bolts helped. Since the engine is clamped into the frame, providing rigidity, messed up mounts can cause handling problems too.