The Mu2e experiment at Fermilab proposes to measure the ratio of the rate of neutrinoless coherent conversion of muons into electrons in the field of a nucleus, relative to the rate of muon capture on the nucleus. The conversion process is an example of charged lepton flavor violation. Observation of this process would provide unambiguous evidence for physics beyond the Standard Model. The design of the experiment is based on three superconducting solenoid magnets. The most important uncertainties in the magnetic field of the solenoids can arise from misalignments of the Transport Solenoid, which transfers the beam from the muon production area to the detector area and eliminates beam-originating backgrounds. In this work, the field uncertainties induced by possible misalignments and their impact on the physics parameters of the experiment are examined. The physics parameters include the muon and pion stopping rates and the scattering of beam electrons off the capture target, which determine the signal, intrinsic background and late-arriving background yields, respectively. Additionally, a possible test of the Transport Solenoid alignment with low momentum electrons is examined, as an alternative option to measure its field with conventional probes, which is technically difficult due to mechanical interference.