hi,i am putting my thoughts/reply below in blue
1.) You said that you are looking to analyze a cantilever column, which you split into two elements (3 nodes). When you do this you should only have a 4x4 stiffness matrix due to the boundary condition of the fixed support. Considering the other two nodes, each will have two DOF, a lateral displacement and a rotation. The whole structure is divided into 2 beam elements (actually frame) with 3 DOFs at each node (2 lateral and 1 rotation)- considering one single plane.so for element, its a 6x6 matrix, I combined the element matrices to get 9x9 matrix for the global stiffness matrix, then chopped out rows/columns from 1 to 3 as my initial node has no translations/rotations. I am pretty sure about the global [K] matrix as I modeled the same cantilever in sacs software, applied a load, found the deflection, and this is matching the deflection when I worked it out using disp=[K_1]*{F}.. it was matching exactly the software output.
2.) I also noticed in the stiffness matrix that you had the axial stiffness of the cantilever column included as well. Due to the direction of the motion of the cantilever, this is not necessary and will over complicate your analysis. Unless the motion you are looking to analyze is along the the column longitudinal axis. I was considering axial load on the top when I checked the deflection, so included axial stiffness also, as said in point 1, the dof for frame was considered, not that of a beam.
2.) The mass matrix should be a diagonal matrix. Considering the column to be split into two elements, you should have two lumped masses. I was using consistent mass approach, and I verified the natural timeperiod with a commericial software, results are matching exact for mode 1. I compared the freq of cantilever for mode 1 in software & on Mathcad, its matching. what I need is how to arrive at mode shape from here.because I have converted the generalized eqn to std Eigen format, I understand that the Eigen values will remain same, but not Eigen vectors, I need to know how to get the Eigen vectors for the real case and then derive the modeshapes.
3.) I would suggest getting a book on structural dynamics, to help explain things further.