Yesterday I finally conquered a similar problem on my K2.
The problem manifested itself on smooth roads, between 45-60 mph, cycling, rhythmic set of bounces felt through the front end and handlebars. I rebuilt the whole front end, went through two brand new sets of tires (thinking I had an out-of-round situation), balanced and rebalanced again, seated and reseated again...nothing.
A few weeks ago I was heading south with the setting sun on my right side when I plainly saw the problem in my shadow...the rear wheel was hopping like mad in the exact cyclic cycle of what I was feeling in my hands and the frame. Time to concentrate on the rear wheel, and maybe the suspension as well. I really hoped the problem was only the wheel, as my shocks are new Hagons, which I love and did not want to change.
The rear wheel was a 16" harley-style conversion rim that took a tremendous amount of weight to balance (like 3.5 ounces!), but it would balance eventually. Yesterday, I changed it out to an 18" wheel of appropriate vintage, and put another freshly-balanced new tire on as well.
Boom! Like butter. That 16" wheel, though balanced, was absolutely not acting like it on the street.
The only explanation that I can come up with now is that the rim itself must not be round. I will be putting it on the truing/balancing stand once the tire is off to find out for sure.
FWIW, and YMMV.
All the best,
Shane