In this thesis, the results of 5 different elliptical cavity designs at different cell numbers and frequencies and the fabrication and measurement of two of these are presented in order to investigate the effects of cell alignment error and surface roughness. First, a 9-cell, 3.9 GHz elliptical cavity with very poor cell-to-cell coupling is designed and the acceleration parameters are optimized. Thanks to the low cell-to-cell coupling, it is aimed to better observe possible mechanical defects and the effects of cell alignment errors in this cavity on the fundamental cavity parameters and particle-cavity interaction are investigated using CST-MWS program. In addition, the effect of surface roughness of the cavity on wake fields and impedances is among the parameters that are tried to be observed. Second, a 3-cell 2 GHz cavity and its scaled version, 3-cell 3.9 GHz cavity, are designed to demonstrate that the effects of cell misalignment were not limited to only this geometry, and similar simulations are repeated for these cavities. In the experimental part of the thesis, a 3-cell 3.9 GHz elliptical cavity with high cell-to-cell coupling is designed and fabricated with a 3D printer and made conductive by nickel and copper coating techniques. Then, the effects of cell misalignment on the quality factor and the electric field on the acceleration axis are investigated experimentally. For these processes, bead-pull measurement is utilized in addition to weak and critical coupling measurements. In the last part, a 2.45 GHz single cell aluminum cavity is fabricated, the same experiments are repeated and it is experimentally demonstrated that similar effects can also be observed with higher conductivity values.