I did a 5k mile round trip this spring on my 07 and had the same issue following/passing semi's. It was really bad. At first, I thought something was terribly wrong with the bike, then like magic it seemed to go away & then come back again at seemingly random times. I had tightened up my head bearing before the trip and was certain it was ok. The other changes made before the trip, were brand new tires and a brand new F4 wide windshield. Both were possible factors in my mind.
Well, 5k miles in the saddle is a good amount of time to figure this out, so here's what I eventually figured out:
1st, it was windy as all heck, going down hiway 5 in CA & then on 40 through AZ & NM, there were signs warning about the wind. Unbelievable wind. Ton's of semi's on the road and the turbulence coming off of them, coupled with the wind, coupled with me going 85+ and I literally never went more than two minutes without seeing a semi, so it was constant turbulence.
Turbulence was dramatically worse within 50 feet of the rear of the semi until I was just past the rear wheels, while passing. Once I got past the rear wheels, the turbulence almost completely died and then as I passed the cab, got blasted by the side wind. It was utterly exhausting. I was speeding up to get through it as fast as possible, but increasing speed only made it worse. It was literally a no-win so I chose faster speed, more turbulence and finish the ride sooner. I did a couple of 3-400 mile days like that and they were exhausting.
On the return route, Hiway 70 through KS, CO & UT, no wind to speak of and I was doing 90++ and she was a stable as could be. Far fewer trucks on 70 than 40, maybe like 90% less, so can't recall that it was ever an issue passing them, leading me to believe that the prevailing winds were the biggest culprit, followed by the extreme turbulence it created off the semi's.
I also suspect that the wider windshield might have come into play, but in the end, my conclusion was the wind was primary factor. And the moral of the story was never ride 40 through AZ & NM again. Ever. Other than Flagstaff, its pretty boring/ugly landscape and unbelievably windy!