It seems that all of your "shakes" are comming with the skids touching the ground, even slightly... Some of the Raptor fliers I have helped back here have experienced similar "shakes"...

We have found that the Raptor landing gear (same thing on my little Voyager E) is quite flexible and the vibrations are being amplified by the landing gear... These guys have replaced their landing gear with MinAir "Tuff Struts" and the slightly beefier struts have gotten rid of their "shakes"...