I too have read about empennage vibrations on the maiden flight, specifically coming from where the vertical stabilizer joined the fuselage.
Flight out-of-ground effect? I think so, just watch the film of the initial flight where the Hercules actually climbs well enough so that Mr. Hughes actually has to input some DOWN control. I don't think that was done to increase airspeed, due to the low altitude. I don't know what flap settings were used, so it may also have been a result of flap retraction and subsequent trim adjustment.