In this work, we investigate the dynamic response of the Maglev vehicle-guideway system at medium-low speed, in the presence of geometric and guideway irregularities. Such irregularities are recognized to be of importance, as they can be linked to the different stiffness of adjacent girders. In the analysis, the vehicle model is a multi-rigid body one while finite elements are adopted for the guideway system to allow for local effects of the F-type rail; the suspension control is instead based on a state observer, to compute the interaction between the vehicle and the guideway system. The ultra-low stiffness steel beam is used for the first time to carry out field tests, featuring a bending stiffness and a weight respectively reduced by 65% and around 80%, if compared to that of the adjacent ordinary concrete beams. The support piers of the steel beams are manually jacked up by 5, 10, 15, and 20 mm during the experimental campaign, to sense the system response and the effects on the suspension gap when the track geometry is uneven due to aforementioned irregularities and to environmental factors. The outcome of field tests and the numerical results have shown that the stiffness of the guideway system and the irregularities have significant effects on the monitored Maglev system. Appropriate arrangements of the stiffness relationship between adjacent girders and a clear matching among guideway, vehicle and suspension control parameters can be then used to effectively reduce the vibrations and improve vehicle comfort.